D1.1 DNA replication: core idea
· DNA replication produces exact copies of DNA with identical base sequences.
· It is essential before cell division, so it is required for reproduction, growth and tissue replacement in multicellular organisms.
· The key exam idea: each original DNA strand acts as a template for a new strand.
This diagram shows the overall process of DNA replication at a replication fork. It helps you visualize strand separation and synthesis of new complementary strands from each original template. Caption/title visible: DNA replication. Source
Semi-conservative replication and complementary base pairing
· Semi-conservative replication means each new DNA molecule contains one original (parental) strand and one newly synthesized strand.
· Accuracy depends on complementary base pairing: A pairs with T, and C pairs with G.
· Because the base sequence on the template determines the new strand, replication is highly accurate.
· Exam wording to use: complementary base pairing ensures a high degree of accuracy in copying base sequences.
Enzymes in standard-level replication
· Helicase unwinds the DNA double helix and breaks hydrogen bonds between complementary bases.
· This separates the two strands and forms a replication fork.
· DNA polymerase builds the new strand by adding complementary DNA nucleotides to the template strand.
· DNA polymerase does not place random bases; it adds nucleotides according to base-pairing rules.
This figure breaks replication into stages on the lagging strand, including helicase action, primer formation, strand extension and sealing. It is especially useful for remembering where RNA primers and DNA ligase fit into the sequence. Source
Polymerase chain reaction (PCR)
· PCR is used to amplify DNA, making many copies of a selected DNA region.
· It requires primers, temperature changes and Taq polymerase.
· Primers mark the start points for copying the target sequence.
· Taq polymerase is heat-stable, so it can keep working after repeated heating cycles.
· The three core stages to know:
· Denaturation: high temperature separates DNA strands.
· Annealing: lower temperature allows primers to bind to target sequences.
· Extension: Taq polymerase adds nucleotides and extends from the primers.
· Repeating these cycles causes rapid DNA amplification.
This image shows the repeating temperature-driven stages of PCR used to copy a target DNA sequence. It is ideal for revising the role of primers, heat cycling and Taq polymerase in amplification. Source
Gel electrophoresis
· Gel electrophoresis is used to separate DNA fragments.
· DNA fragments move through a gel when an electric current is applied.
· DNA is negatively charged, so fragments move toward the positive electrode.
· Smaller DNA fragments move faster and therefore travel further through the gel than larger fragments.
· The pattern of bands can be compared between samples.
Applications of PCR and gel electrophoresis
· Together, PCR and gel electrophoresis are key tools for amplifying and separating DNA.
· Important applications include DNA profiling, especially in paternity testing and forensic investigations.
· In DNA profiling, using more markers reduces the probability of a false match.
· Exam tip: link the technique to the purpose: PCR makes enough DNA, then gel electrophoresis separates fragments for comparison.
HL only: 5' to 3' directionality
· DNA strands have a 5' end and a 3' end.
· DNA polymerases add nucleotides only to the 3' end of a growing strand.
· Therefore, new DNA is always synthesized in the 5' to 3' direction.
· This directionality explains why the two new strands are made differently at the replication fork.
HL only: leading and lagging strands
· On the leading strand, DNA synthesis is continuous because polymerase moves in the same overall direction as fork opening.
· On the lagging strand, DNA synthesis is discontinuous because polymerase still works 5' to 3', but the template runs in the opposite orientation.
· The lagging strand is made in short sections called Okazaki fragments.
· Replication is initiated with an RNA primer once on the leading strand but repeatedly on the lagging strand.
This diagram compares continuous synthesis on the leading strand with discontinuous synthesis on the lagging strand. It is one of the clearest visuals for understanding Okazaki fragments and why the lagging strand needs repeated priming. Source
HL only: enzyme roles in prokaryotic replication
· DNA primase synthesizes the RNA primers needed to start DNA synthesis.
· DNA polymerase III is the main enzyme that adds DNA nucleotides during replication in prokaryotes.
· DNA polymerase I removes RNA primer nucleotides and replaces them with DNA nucleotides.
· DNA ligase joins adjacent DNA fragments by sealing gaps in the sugar-phosphate backbone.
· In the lagging strand, ligase is needed to join Okazaki fragments into one continuous strand.
HL only: DNA proofreading
· DNA polymerase III can carry out proofreading.
· If the base at the 3' terminal is mismatched, polymerase III removes that nucleotide.
· It then replaces it with the correctly matched nucleotide.
· This further increases the accuracy of DNA replication.
Checklist: can you do this?
· Explain why DNA replication is described as semi-conservative.
· State the roles of helicase and DNA polymerase in replication.
· Interpret why smaller DNA fragments move further in gel electrophoresis.
· Outline the stages of PCR and the role of primers and Taq polymerase.
· For HL, compare the leading and lagging strands and name the roles of primase, DNA polymerase I, DNA polymerase III and ligase.
Exam traps to avoid
· Do not say replication is conservative; it is semi-conservative.
· Do not confuse hydrogen bonds breaking with breaking the sugar-phosphate backbone; helicase separates strands by breaking hydrogen bonds only.
· Do not say DNA polymerase works 3' to 5'; synthesis is always 5' to 3'.
· Do not confuse PCR with gel electrophoresis: PCR amplifies, gel electrophoresis separates.
· Do not forget that proofreading and the named roles of polymerase I/III, primase and ligase are HL only.
Shubhi is a seasoned educational specialist with a sharp focus on IB, A-level, GCSE, AP, and MCAT sciences. With 6+ years of expertise, she excels in advanced curriculum guidance and creating precise educational resources, ensuring expert instruction and deep student comprehension of complex science concepts.
Shubhi is a seasoned educational specialist with a sharp focus on IB, A-level, GCSE, AP, and MCAT sciences. With 6+ years of expertise, she excels in advanced curriculum guidance and creating precise educational resources, ensuring expert instruction and deep student comprehension of complex science concepts.