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IB DP Biology D1.1 DNA replication Study Notes | IITian Academy

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

IBDP Biology 2025 -Study Notes -All Topics

D1.1.1—DNA replication as production of exact copies of DNA with identical base sequences

  • Importance of Replication: DNA replication is crucial for two essential biological processes:

    1. Reproduction: Offspring inherit genetic information from their parents. Therefore, DNA replication is necessary for parents to pass on their DNA to their offspring.
    2. Growth and Tissue Repair: In multicellular organisms, every cell needs a complete set of the organism’s DNA. Before a cell divides, it must replicate its DNA to ensure that each daughter cell receives a full set of genetic information. This is essential for growth and replacing cells that are lost or damaged (e.g., skin cells).

  • Accuracy of Replication: DNA’s structure allows for highly accurate replication. This ensures the continuity of life across generations.

DNA replication is a fundamental process that ensures the faithful transmission of genetic information from one generation to1 the next and is essential for growth and development in multicellular organisms.

D1.1.2—Semi-conservative nature of DNA replication and role of complementary base pairing

When DNA is replicated, the two strands of the double helix must separate. Both original strands serve as templates to guide the polymerization of a new strand. The new strands are formed by adding nucleotides one by one and linking them together. This happens progressively along a DNA molecule. The site at which the copying is actively occurring is a replication fork. When replication is complete, there are two DNA molecules, each composed of an original strand and a newly synthesized strand. For this reason, DNA replication is referred to as semi-conservative.

The base sequence on the template strand determines the base sequence on the new strand. Only a nucleotide carrying a base that is complementary to the next base on the template strand can successfully be added to the new strand.1 This is because complementary bases form hydrogen bonds with each other, stabilizing the structure. If a nucleotide with the wrong2 base were inserted, hydrogen bonding between bases would not occur and the nucleotide would be rejected. Adenine pairs with thymine, not cytosine or guanine, and cytosine only pairs with guanine.

The rule that one base always pairs with another is called complementary base pairing. It ensures that the two DNA molecules3 resulting from DNA replication are identical in their base sequences to the parent molecule.4 Complementary base pairing ensures a high degree of accuracy when new strands are assembled on a template strand. It also makes it possible to check the base sequence that has been assembled, recognize any mispairing, then cut out and replace the incorrect nucleotides. These processes together ensure that only about 1 in 10 billion bases is incorrect when DNA is replicated.

A diploid human cell has DNA with approximately 6 billion base pairs, so on average there are only 0.6 errors when all the DNA is replicated prior to mitosis.

Additional Information:

  • Importance of Semi-Conservative Replication: Semi-conservative replication ensures that each daughter cell receives a complete and accurate copy of the genetic information from the parent cell. This5 is crucial for maintaining genetic stability and preventing errors that could lead to mutations and diseases.
  • Enzymes Involved in Replication: Several enzymes play key roles in DNA replication, including:
    • Helicase: Unwinds the double helix to separate the two strands.
    • DNA Polymerase: Synthesizes the new DNA strand by adding nucleotides to the growing chain.
    • Primase: Synthesizes short RNA primers to initiate DNA synthesis.
    • Ligase: Joins the fragments of DNA synthesized on the lagging strand.
  • Proofreading and Repair Mechanisms: In addition to complementary base pairing, cells have various mechanisms to proofread and repair errors that may occur during DNA replication. These mechanisms help to ensure the high fidelity of DNA replication.

Semi-conservative replication is a fundamental process that ensures the faithful transmission of genetic information from one generation to the next. It is a highly accurate process due to the principles of complementary base pairing and the presence of proofreading and repair mechanisms.

D1.1.3—Role of helicase and DNA polymerase in DNA replication

Key Points:

  • DNA Replication as a Multi-Stage Process: DNA replication is a complex process involving multiple enzymes and proteins. The replisome is a large protein complex that carries out DNA replication.
  • Role of Helicase:
    • Helicase is an enzyme that unwinds the double-stranded DNA helix.
    • It acts like a “zipper,” breaking the hydrogen bonds between the base pairs of the two strands.
    • This unwinding creates a replication fork, where DNA synthesis can begin.
    • Helicase separates the two strands, allowing each to serve as a template for the synthesis of a new complementary strand.

  • Role of DNA Polymerase:
    • DNA polymerase is the enzyme responsible for synthesizing the new DNA strands.
    • It moves along the template strand, adding nucleotides one by one to the growing new strand.
    • Only nucleotides with complementary bases can be added to the growing strand.
    • DNA polymerase forms a covalent bond between the incoming nucleotide and the existing strand, extending the new DNA strand.

Helicase and DNA polymerase are two essential components of the replisome. Helicase unwinds the DNA helix, while DNA polymerase synthesizes the new DNA strands, ensuring accurate replication of the genetic information.

D1.1.4—Polymerase chain reaction and gel electrophoresis as tools for amplifying and separating DNA

Polymerase chain reaction

  • Amplification of DNA: PCR is a powerful technique used to amplify specific DNA sequences.
  • Components:
    • DNA Template: The DNA containing the target sequence to be amplified.
    • Primers: Short, single-stranded DNA sequences that bind to specific regions on the template DNA, flanking the target sequence. Primers are typically 18-30 nucleotides long.
    • Taq DNA Polymerase: A heat-stable DNA polymerase enzyme isolated from the thermophilic bacterium Thermus aquaticus. It can withstand the high temperatures used in PCR.
    • dNTPs: Deoxynucleoside triphosphates (dATP, dTTP, dCTP, dGTP) – the building blocks of DNA.
  • Process:
    1. Denaturation: The reaction mixture is heated to a high temperature (around 95°C) to denature the double-stranded DNA template into single strands.
    2. Annealing: The temperature is lowered (around 55-65°C) to allow the primers to anneal (bind) to their complementary sequences on the single-stranded DNA templates.
    3. Extension: The temperature is raised to the optimal temperature for Taq DNA polymerase activity (around 72°C). Taq polymerase synthesizes new DNA strands by adding nucleotides to the primers, extending the DNA sequence.
  • Cycling: These three steps (denaturation, annealing, and extension) are repeated for multiple cycles (typically 25-35 cycles) in a thermal cycler. Each cycle doubles the number of copies of the target DNA sequence.

PCR is a powerful technique for amplifying specific DNA sequences, while gel electrophoresis is used to separate DNA fragments based on their size, enabling researchers to analyze and visualize DNA samples.

 

 Gel electrophoresis

  • Separation of DNA Fragments: Gel electrophoresis is a technique used to separate DNA fragments based on their size.
  • Process:
    1. Gel Preparation: An agarose gel is prepared. The gel is placed in an electrophoresis tank filled with a buffer solution.
    2. Sample Loading: DNA samples are loaded into wells at one end of the gel.
    3. Electrophoresis: An electric current is applied across the gel. DNA fragments, being negatively charged due to the phosphate backbone, migrate towards the positive electrode (anode).
    4. Separation: Smaller DNA fragments move through the gel matrix more easily than larger ones, resulting in the separation of DNA fragments based on their size.
    5. Visualization: After electrophoresis, the gel is stained with a dye that binds to DNA, making the DNA bands visible.
  • DNA Ladder: A DNA ladder containing fragments of known sizes is typically loaded in a separate well. This ladder allows for the estimation of the sizes of DNA fragments in the other samples.

D1.1.5—Applications of polymerase chain reaction and gel electrophoresis

1. Testing for Coronaviruses:

  • Sample Collection: A swab is taken from the nose or throat to collect a sample containing viral particles and viral RNA.
  • RNA to DNA Conversion: The viral RNA in the sample is converted into DNA using the enzyme reverse transcriptase. This process is called reverse transcription.
  • PCR Amplification: PCR is then used to amplify specific viral DNA sequences that are characteristic of the coronavirus strain being tested for. Multiple cycles of PCR are performed, typically around 35 cycles.
  • Detection: As PCR progresses, fluorescent markers are attached to the newly synthesized DNA. The level of fluorescence is monitored. If the level of fluorescence rises above a target level, the test result for the coronavirus is considered positive.

Advantages of PCR Testing for Coronaviruses:

  • High Sensitivity: PCR can detect even minute quantities of viral RNA in a sample due to the amplification process.
  • High Specificity: Primers can be designed to target specific viral strains, ensuring accurate detection.

Disadvantages of PCR Testing for Coronaviruses:

  • Cost and Equipment: The equipment and materials required for PCR testing can be relatively expensive.
  • Time Requirement: The thermal cycling process takes time, so results may not be available immediately.

2. DNA Profiling for Paternity Testing:

Certainly, let’s explore the process of DNA profiling for paternity testing as depicted in the image.

Key Points:

  • Short Tandem Repeats (STRs): DNA profiling relies on the analysis of variations in the number of short tandem repeats (STRs) in an individual’s DNA. STRs are short DNA sequences (usually 2-7 base pairs) that are repeated consecutively multiple times.
  • Variability in STR Repeats: The number of repeats of each STR varies considerably between individuals. This variability is the basis for distinguishing individuals based on their DNA profiles.
  • DNA Profiling Procedure:
    1. DNA Extraction: A DNA sample is obtained from the child, the mother, and the alleged father.
    2. PCR Amplification: Specific STR loci are selected, and the corresponding DNA fragments are amplified using PCR.
    3. Gel Electrophoresis: The PCR products are separated based on their size using gel electrophoresis. This generates a unique pattern of bands for each individual.
    4. Comparison of Profiles: The DNA profiles of the child, mother, and alleged father are compared. If any bands in the child’s profile do not match either the mother’s or the alleged father’s profile, it is strong evidence that the alleged father is not the biological father.

Reasons for Paternity Testing:

  • Establishing Legal Paternity: To determine legal rights and responsibilities of the father.
  • Child Support: To establish child support obligations.
  • Inheritance Rights: To determine inheritance rights for the child.
  • Peace of Mind: To confirm or rule out paternity for personal reasons.

DNA profiling for paternity testing utilizes the unique pattern of STR repeats in an individual’s DNA to determine biological parentage with a high degree of accuracy.

D1.1.6—Directionality of DNA polymerases

Key Points:

  • Nucleotide Structure and Bonding:

    • Nucleotides are the building blocks of DNA. Each nucleotide consists of a sugar (deoxyribose), a phosphate group, and a nitrogenous base1 (adenine, guanine, cytosine, or thymine).2
    • The sugar in a nucleotide has a 5′ carbon and a 3′ carbon.
    • The phosphate group is attached to the 5′ carbon of the sugar.
    • The hydroxyl group (-OH) attached to the 3′ carbon of the sugar is available for forming a covalent bond with another nucleotide.

  • Directionality of DNA Synthesis:

    • DNA polymerases can only add nucleotides to the 3′ end of a growing DNA strand.
    • This means that DNA synthesis always proceeds in the 5′ to 3′ direction.

 

      • DNA polymerases add a new nucleotide by forming a covalent bond between the 5′ phosphate group of the incoming nucleotide and the 3′ hydroxyl group of the last nucleotide in the growing strand.

  • Implications for DNA Replication:

    • The 5′ to 3′ directionality of DNA synthesis has important implications for DNA replication.
    • Since DNA polymerases can only add nucleotides to the 3′ end, the two strands of the DNA double helix are synthesized in opposite directions.

The directionality of DNA synthesis is a fundamental property of DNA polymerases. This directionality has significant implications for the mechanisms of DNA replication and repair.

D1.1.7—Differences between replication on the leading strand and the lagging strand

Key Points:

  • Antiparallel Strands: The two strands of the DNA double helix are antiparallel, meaning they run in opposite directions. One strand has a 5′ to 3′ orientation, while the other has a 3′ to 5′ orientation.
  • Directionality of DNA Polymerase: DNA polymerase can only synthesize new DNA strands in the 5′ to 3′ direction. This means it can only add nucleotides to the 3′ end of the growing strand.

Leading Strand Synthesis:

  • Continuous Synthesis: On one strand, the leading strand, DNA polymerase moves in the same direction as the replication fork.
  • Continuous Replication: Since DNA polymerase moves in the same direction as the replication fork, it can synthesize the new strand continuously without interruption.

Lagging Strand Synthesis:

  • Discontinuous Synthesis: On the other strand, the lagging strand, DNA polymerase moves in the opposite direction of the replication fork.
  • Okazaki Fragments: As the replication fork opens, DNA polymerase must synthesize the new strand in short fragments called Okazaki fragments. This is because it can only add nucleotides in the 5′ to 3′ direction.

  • Discontinuous Process: The need to synthesize the lagging strand in short fragments and then join them together makes the process of replication on the lagging strand slower than on the leading strand.

The antiparallel nature of the DNA strands and the 5′ to 3′ directionality of DNA polymerase lead to differences in the replication process on the leading and lagging strands.

 

 

D1.1.8—Functions of DNA primase, DNA polymerase I, DNA polymerase III and DNA ligase in replication

Key Points:

  • Replisome: A Multi-protein Complex: The replisome is a large protein complex that carries out DNA replication. It includes multiple enzymes and proteins that work together to unwind the DNA, synthesize new strands, and proofread the newly synthesized DNA.
  • Helicase: Helicase is a ring-shaped enzyme that unwinds the double-stranded DNA helix by breaking the hydrogen bonds between the base pairs. It creates a replication fork where DNA synthesis can begin.
  • DNA Primase: DNA primase is a type of RNA polymerase. It synthesizes a short RNA primer on the template strand. This RNA primer provides a starting point for DNA polymerase III to bind and begin adding DNA nucleotides.
  • DNA Polymerase III: This is the main enzyme responsible for DNA synthesis. It adds DNA nucleotides to the 3′ end of the growing DNA strand, moving in the 5′ to 3′ direction. DNA polymerase III also has a proofreading function, ensuring the accuracy of DNA replication.
  • Lagging Strand Synthesis: On the lagging strand, DNA synthesis occurs in short fragments called Okazaki fragments. DNA primase synthesizes multiple RNA primers along the lagging strand, and DNA polymerase III synthesizes short stretches of DNA between these primers.
  • DNA Polymerase I: DNA polymerase I removes the RNA primers and replaces them with DNA nucleotides. It also has a proofreading function.
  • DNA Ligase: DNA ligase seals the gaps between the Okazaki fragments by forming phosphodiester bonds between the adjacent nucleotides.

The replisome is a complex machinery that coordinates the various steps involved in DNA replication, ensuring the accurate and efficient duplication of the genetic material.

D1.1.9—DNA proofreading

Key Points:

  • High Fidelity of DNA Replication: DNA polymerases are highly accurate enzymes, but they can occasionally make errors during DNA synthesis, leading to the incorporation of incorrect nucleotides (mismatches).
  • DNA Proofreading: To minimize errors, DNA polymerases have a built-in proofreading mechanism.
  • Process of Proofreading:
    1. Mismatch Detection: If DNA polymerase detects a mismatch between the newly added nucleotide and the base on the template strand, it pauses DNA synthesis.
    2. Exonuclease Activity: DNA polymerase III has an exonuclease activity, meaning it can remove the most recently added nucleotide.
    3. Backtracking: After removing the incorrect nucleotide, DNA polymerase moves back along the template strand by one nucleotide.
    4. Correct Insertion: DNA polymerase then inserts the correct nucleotide, ensuring that the newly synthesized DNA strand is accurate.

Significance of Proofreading:

  • Reducing Mutations: Proofreading significantly reduces the frequency of errors during DNA replication, minimizing the risk of mutations.
  • Maintaining Genetic Stability: Accurate DNA replication is crucial for maintaining the integrity of the genetic information and preventing genetic diseases.

DNA proofreading is an essential quality control mechanism that ensures the high fidelity of DNA replication. It helps to maintain the integrity of the genome and prevent the accumulation of mutations.

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