IB DP Biology D1.1 DNA replication Study Notes - New Syllabus -2025
IB DP Biology D1.1 DNA replication Study Notes – New syllabus 2025
IB DP Biology D1.1 DNA replication Study Notes at IITian Academy focus on specific topic and type of questions asked in actual exam. Study Notes focus on IB Biology syllabus with guiding questions of
- How is new DNA produced?
- How has knowledge of DNA replication enabled applications in biotechnology?
Standard level and higher level: 2 hours
Additional higher level: 2 hours
D1.1.1 – DNA Replication: Making Exact Copies of DNA
🔍 What is DNA Replication?
- DNA replication is the process of producing exact copies of DNA.
- The copies have identical base sequences to the original DNA strand.
- This ensures genetic information is faithfully passed on.
🌱 Why is DNA Replication Important?
Reproduction: In both unicellular and multicellular organisms, DNA replication is essential before cell division to pass genetic information to offspring.
Growth: New cells for body growth require exact DNA copies.
Tissue Replacement: Damaged or old cells are replaced with new ones having the same DNA.
⚙️ Key Point
DNA replication maintains genetic continuity, preserving traits across generations and within an organism.
DNA replication produces identical copies of DNA, crucial for reproduction, growth, and repair in living organisms.
D1.1.2 – Semi-Conservative DNA Replication & Complementary Base Pairing
⚙️ Semi-Conservative Replication
- Each new DNA molecule contains:
One original (parental) strand
One newly synthesized strand - This method ensures genetic accuracy and stability.
🧩 Complementary Base Pairing
- DNA bases pair specifically:
Adenine (A) with Thymine (T)
Cytosine (C) with Guanine (G) - During replication, each original strand serves as a template.
- New nucleotides pair with their complementary bases on the template strand.
🎯 High Accuracy Mechanism
- Complementary base pairing allows DNA polymerase enzymes to add the correct nucleotides.
- This results in very accurate copying of the base sequence.
- Proofreading enzymes further reduce errors during replication.
🔬 Why It Matters
Maintains the integrity of genetic information across generations.
Prevents mutations that could harm cells or organisms.
DNA replication is semi-conservative, producing one old and one new strand per molecule. Complementary base pairing ensures high-fidelity copying of genetic information.
D1.1.3 – Roles of Helicase and DNA Polymerase in DNA Replication
🧩 Helicase: The DNA Unwinder
- Helicase breaks hydrogen bonds between complementary DNA bases.
- This action unwinds the double helix, separating the two strands.
- Creates the replication fork, where new strands can be synthesized.
🛠️ DNA Polymerase: The Builder
- DNA polymerase adds new nucleotides to the exposed single strands.
- It uses each original strand as a template.
- Catalyzes the formation of phosphodiester bonds, linking nucleotides into a new strand.
- Works in a specific direction (5′ to 3′) to build the DNA strand.
🔑 Key Points
- Helicase opens the DNA helix.
- DNA polymerase assembles the new complementary strand.
- Both enzymes are essential for accurate DNA replication.
Helicase unwinds DNA by breaking hydrogen bonds, while DNA polymerase builds new DNA strands by adding nucleotides complementary to the template strand.
D1.1.4 – PCR and Gel Electrophoresis: Amplifying and Separating DNA
🔄 Polymerase Chain Reaction (PCR)
PCR is a technique to amplify (make many copies) of a specific DNA segment.
Key components:
- Primers: Short DNA sequences that bind to target regions on DNA, marking start points for replication.
- Taq polymerase: Heat-stable enzyme that synthesizes new DNA strands.
Temperature changes control the stages:
- Denaturation (~95°C): DNA strands separate by breaking hydrogen bonds.
- Annealing (~50-65°C): Primers bind (anneal) to target sequences.
- Extension (~72°C): Taq polymerase adds nucleotides to build new strands.
This cycle repeats 20-40 times, exponentially increasing DNA copies.
🧪 Gel Electrophoresis
- Technique to separate DNA fragments by size.
- DNA samples are placed in a gel matrix and an electric current is applied.
- DNA is negatively charged and moves towards the positive electrode.
- Smaller fragments travel faster and farther through the gel than larger ones.
- After separation, DNA bands can be visualized using dyes or UV light.
📋 Summary Table
| Technique | Purpose | Key Features |
|---|---|---|
| PCR | Amplify specific DNA segments | Uses primers, Taq polymerase, temperature cycles |
| Gel Electrophoresis | Separate DNA fragments by size | DNA moves through gel by size; smaller fragments travel further |
PCR amplifies DNA using primers, Taq polymerase, and thermal cycles, while gel electrophoresis separates DNA fragments by size based on their movement through a gel under an electric field.
D1.1.5 – Applications of PCR and Gel Electrophoresis
🔍 Uses of PCR and Gel Electrophoresis
- DNA Profiling:
Used in forensic investigations to identify individuals from biological samples.
Helps establish paternity by comparing DNA markers. - Medical Diagnostics:
Detects genetic diseases by amplifying specific DNA sequences. - Biological Research:
Study genes and mutations.
Analyze genetic diversity in populations.
🧪 Enhancing Reliability in DNA Profiling
Using multiple DNA markers reduces chances of false matches.
Increasing the number of measurements/tests improves accuracy.
Important for ensuring trustworthy forensic and paternity results.
📌 Key Point
PCR combined with gel electrophoresis provides a powerful toolkit for identifying and analyzing DNA with wide-ranging real-world applications.
PCR and gel electrophoresis enable DNA profiling, forensic analysis, and medical diagnostics. Reliability improves by increasing markers and repeated testing.
D1.1.6 – Directionality of DNA Polymerases
🔄 DNA Strand Directionality
DNA strands have two distinct ends:
- 5′ (five prime) end with a phosphate group
- 3′ (three prime) end with a hydroxyl group (-OH)
These ends give DNA strands a direction, important for replication.
🛠️ How DNA Polymerase Works
- DNA polymerases add nucleotides only to the 3′ end of the growing DNA strand.
- This means nucleotides are joined 5′ phosphate of the incoming nucleotide to the 3′ hydroxyl of the existing strand.
- DNA replication proceeds in the 5′ to 3′ direction along the new strand.
🎯 Why Direction Matters
The enzyme’s directionality ensures DNA is copied accurately and efficiently.
It also causes differences in replication on the two strands (leading and lagging strands).
DNA polymerase adds nucleotides to the 3′ end of a DNA strand, joining the 5′ phosphate of the new nucleotide to the 3′ hydroxyl of the strand, meaning replication proceeds 5′ to 3′.
D1.1.7 – Differences Between Replication on the Leading and Lagging Strands
🔀 DNA Strands Are Antiparallel
DNA strands run in opposite directions:
- One strand: 5′ → 3′ (leading strand direction)
- Other strand: 3′ → 5′ (lagging strand direction)
DNA polymerase works only 5′ → 3′ when synthesizing new DNA.
➡️ Leading Strand Replication
Continuous synthesis:
- DNA polymerase moves in the same direction as the replication fork.
- New DNA is made smoothly and continuously.
- Only one RNA primer is needed at the start.
⬅️ Lagging Strand Replication
Discontinuous synthesis:
- DNA polymerase moves opposite to the replication fork’s direction.
- Synthesizes DNA in short fragments called Okazaki fragments.
- Requires multiple RNA primers, one for each Okazaki fragment.
- Fragments are later joined by DNA ligase.
| Strand | Synthesis Type | RNA Primers Required | Fragments Formed |
|---|---|---|---|
| Leading strand | Continuous | One | None |
| Lagging strand | Discontinuous | Multiple | Okazaki fragments |
Leading strand replication is continuous with a single RNA primer, while lagging strand replication is discontinuous, forming Okazaki fragments with multiple RNA primers due to DNA polymerase’s 5′ to 3′ directionality.
D1.1.8 – Functions of DNA Primase, DNA Polymerase I, DNA Polymerase III, and DNA Ligase in Prokaryotic DNA Replication
🔹 DNA Primase
- An RNA polymerase enzyme.
- Synthesizes a short RNA primer on the DNA template.
- This primer acts as a starting point for DNA synthesis by DNA polymerase III.
🔹DNA Polymerase III
- The main enzyme for DNA synthesis.
- Adds DNA nucleotides to the 3′ end of the new strand.
- Works in the 5′ to 3′ direction.
- Has a proofreading function to ensure accuracy.
- Synthesizes DNA continuously on the leading strand and discontinuously on the lagging strand.
🔹 DNA Polymerase I
- Removes RNA primers from the new DNA strand.
- Replaces RNA primers with DNA nucleotides.
- Also proofreads to maintain accuracy.
🔹 DNA Ligase
- Seals the gaps between Okazaki fragments on the lagging strand.
- Forms phosphodiester bonds between adjacent nucleotides.
- Ensures a continuous DNA strand.
🔄 Replication Overview (Prokaryotic)
| Enzyme | Role |
|---|---|
| DNA Primase | Synthesizes RNA primers |
| DNA Polymerase III | Adds DNA nucleotides and proofreads |
| DNA Polymerase I | Removes RNA primers, replaces with DNA |
| DNA Ligase | Joins Okazaki fragments by sealing gaps |
DNA primase creates primers, DNA polymerase III extends DNA strands, DNA polymerase I removes primers and fills gaps, and DNA ligase seals Okazaki fragments for continuous DNA strands in prokaryotic replication.
D1.1.9 – DNA Proofreading by DNA Polymerase III
Why Proofreading Is Important
DNA replication is very accurate but errors (mismatches) can sometimes happen.
Proofreading reduces mistakes, helping to prevent mutations and maintain genetic stability.
How DNA Polymerase III Proofreads
- Mismatch Detection: DNA polymerase III pauses when a wrong nucleotide is added.
- Exonuclease Activity: Removes the incorrect nucleotide from the 3′ end (3’→5′ exonuclease function).
- Backtracking: Moves back one nucleotide.
- Correct Replacement: Inserts the correct nucleotide and resumes synthesis.
🔹 Key Points Summary
| Step | Description |
|---|---|
| Detection | Polymerase identifies mismatched base |
| Removal | Exonuclease removes wrong nucleotide |
| Backtracking | Moves back 1 nucleotide |
| Correction | Inserts correct nucleotide |
DNA polymerase III proofreads newly added nucleotides by removing mismatches and replacing them with correct bases, ensuring high accuracy in DNA replication.