CIE AS/A Level Biology -6.1 Structure of nucleic acids and replication of DNA- Study Notes- New Syllabus
CIE AS/A Level Biology -6.1 Structure of nucleic acids and replication of DNA- Study Notes- New Syllabus
Ace A level Biology Exam with CIE AS/A Level Biology -6.1 Structure of nucleic acids and replication of DNA- Study Notes- New Syllabus
Key Concepts:
- describe the structure of nucleotides, including the phosphorylated nucleotide ATP (structural formulae are not expected)
- state that the bases adenine and guanine are purines with a double ring structure, and that the bases cytosine, thymine and uracil are pyrimidines with a single ring structure (structural formulae for bases are not expected)
- describe the structure of a DNA molecule as a double helix, including:
• the importance of complementary base pairing between the 5′ to 3′ strand and the 3′ to 5′ strand (antiparallel strands)
• differences in hydrogen bonding between C–G and A–T
base pairs
• linking of nucleotides by phosphodiester bonds - describe the semi-conservative replication of DNA during the S phase of the cell cycle, including:
• the roles of DNA polymerase and DNA ligase (knowledge of other enzymes in DNA replication in cells and different types of DNA polymerase is not expected)
• the differences between leading strand and lagging strand replication as a consequence of DNA polymerase adding nucleotides only in a 5′ to 3′ direction - describe the structure of an RNA molecule, using the example of messenger RNA (mRNA
Structure of Nucleotides & ATP
🌱 Nucleotides – Basic Unit of Nucleic Acids
- Definition: Nucleotides are the monomers (building blocks) of nucleic acids (DNA & RNA).
- Each nucleotide is made of three main components:
- Nitrogenous Base
Organic molecule containing nitrogen.
Two types:- Purines (double ring): Adenine (A), Guanine (G)
- Pyrimidines (single ring): Cytosine (C), Thymine (T in DNA), Uracil (U in RNA)
- Pentose Sugar
5-carbon sugar.
Deoxyribose in DNA, Ribose in RNA. - Phosphate Group
One or more phosphate groups attached to carbon 5 of sugar.
Negatively charged → makes nucleotide soluble in water.
- Nitrogenous Base
🔬 Nucleotide Structure Overview
| Component | Function |
|---|---|
| Nitrogenous base | Stores genetic code in sequence |
| Pentose sugar | Forms the backbone with phosphate (sugar-phosphate chain) |
| Phosphate group | Links nucleotides together via phosphodiester bonds |
⚡ Phosphorylated Nucleotides
- Nucleotides can have 1, 2, or 3 phosphate groups:
- Monophosphate – AMP (Adenosine Monophosphate)
- Diphosphate – ADP (Adenosine Diphosphate)
- Triphosphate – ATP (Adenosine Triphosphate)
🔋 ATP – Adenosine Triphosphate
- Structure: Adenine (base) + Ribose (sugar) + Three phosphate groups in a chain.
- High-energy bonds between the last two phosphate groups release energy when broken (hydrolysis).
- Function: Main energy currency of the cell. Hydrolysis of ATP → ADP + Pi + energy for cellular processes.
📊 Comparison Table: Nucleotide vs ATP
| Feature | Nucleotide | ATP |
|---|---|---|
| Components | Base + sugar + phosphate | Base (adenine) + ribose + 3 phosphates |
| Function | DNA/RNA building block | Energy transfer in cells |
| Phosphate groups | 1 | 3 |
| Example | Cytidine monophosphate (CMP) | Adenosine triphosphate (ATP) |
🧠 Key Takeaways:
– Nucleotides are made of a nitrogenous base, a pentose sugar, and phosphate group(s).
– ATP is a special nucleotide with three phosphates, storing energy in its bonds.
– Hydrolysis of ATP releases usable energy for cellular activities.
– Nucleotides are made of a nitrogenous base, a pentose sugar, and phosphate group(s).
– ATP is a special nucleotide with three phosphates, storing energy in its bonds.
– Hydrolysis of ATP releases usable energy for cellular activities.
Purines & Pyrimidines – Nitrogenous Bases
🌱 Nitrogenous Bases in Nucleic Acids
- Nitrogenous bases are part of nucleotides in DNA and RNA.
- They are heterocyclic (ring-containing) molecules with nitrogen atoms.
- Two main groups based on their ring structure:
🟢 Purines – Double Ring Structure
- Adenine (A) and Guanine (G).
- Larger molecules with two fused rings (one 6-membered + one 5-membered).
- Found in both DNA and RNA.
🟡 Pyrimidines – Single Ring Structure
- Cytosine (C), Thymine (T), and Uracil (U).
- Smaller molecules with one 6-membered ring.
- Cytosine → found in both DNA and RNA.
- Thymine → found only in DNA.
- Uracil → found only in RNA (replaces thymine).
| Feature | Purines | Pyrimidines |
|---|---|---|
| Bases | Adenine (A), Guanine (G) | Cytosine (C), Thymine (T), Uracil (U) |
| Ring Structure | Double ring (2 fused rings) | Single ring |
| Size | Larger | Smaller |
| Present in | DNA & RNA | DNA & RNA (T only in DNA, U only in RNA) |
🧠 Key Takeaways:
– Adenine & Guanine → Purines → double ring.
– Cytosine, Thymine, Uracil → Pyrimidines → single ring.
– DNA uses A, G, C, T while RNA uses A, G, C, U.
– Adenine & Guanine → Purines → double ring.
– Cytosine, Thymine, Uracil → Pyrimidines → single ring.
– DNA uses A, G, C, T while RNA uses A, G, C, U.
Structure of the DNA Molecule
🌱 Overall Shape – Double Helix
- DNA is a double-stranded molecule twisted into a double helix.
- The two strands run in opposite directions → antiparallel:
- One strand runs 5′ → 3′
- The other runs 3′ → 5′
- Each strand has a sugar-phosphate backbone with nitrogenous bases pointing inward.
🧩 Complementary Base Pairing
- Bases pair through hydrogen bonds:
- Adenine (A) → Thymine (T) → 2 hydrogen bonds
- Cytosine (C) → Guanine (G) → 3 hydrogen bonds
- Purine always pairs with pyrimidine → keeps helix stable and uniform.
- Ensures accurate DNA replication and transcription.
🔗 Phosphodiester Bonds – Backbone Linkage
- Formed between the phosphate group of one nucleotide and the 3′ carbon of the sugar in the next nucleotide.
- Create a sugar-phosphate backbone that is strong and stable.
- Covalent bonds → resistant to breaking.
📊 Summary Table: DNA Structural Features
| Feature | Description | Importance |
|---|---|---|
| Double helix | Two strands twisted | Stability & compact storage |
| Antiparallel strands | 5′ → 3′ and 3′ → 5′ | Correct base pairing & replication |
| Complementary base pairing | A–T (2 bonds), C–G (3 bonds) | Accuracy in copying genetic info |
| Phosphodiester bonds | Sugar–phosphate linkage | Strong backbone support |
🧠 Key Takeaways:
– DNA has two antiparallel strands forming a double helix.
– A–T pairs have 2 hydrogen bonds; C–G pairs have 3, making them stronger.
– Phosphodiester bonds hold nucleotides together in each strand’s backbone.
– Complementary base pairing ensures DNA’s accuracy in replication and transcription.
– DNA has two antiparallel strands forming a double helix.
– A–T pairs have 2 hydrogen bonds; C–G pairs have 3, making them stronger.
– Phosphodiester bonds hold nucleotides together in each strand’s backbone.
– Complementary base pairing ensures DNA’s accuracy in replication and transcription.
Semi-Conservative DNA Replication (S Phase of the Cell Cycle)
🌱 Overview
- Semi-conservative means: after replication, each new DNA molecule has one original (parental) strand and one newly synthesised strand.
- Occurs during the S phase (synthesis phase) of interphase in the cell cycle.
- Ensures accurate copying of genetic material before cell division.
🧬 Step-by-Step Process
1. Strand Separation
- The two DNA strands unwind and separate (hydrogen bonds between bases break).
- Each parental strand acts as a template for the new strand.
2. Nucleotide Pairing
- Free DNA nucleotides in the nucleus pair with exposed bases on each template strand using complementary base pairing:
- A pairs with T (2 hydrogen bonds)
- C pairs with G (3 hydrogen bonds)
3. Role of DNA Polymerase
- Joins new nucleotides together, forming the sugar-phosphate backbone by phosphodiester bonds.
- Can only add nucleotides in the 5′ → 3′ direction.
4. Leading vs Lagging Strand
- Leading strand: Synthesised continuously in the same direction as the unwinding fork.
- Lagging strand: Synthesised discontinuously in short fragments (Okazaki fragments) because DNA polymerase works only 5′ → 3′.
5. Role of DNA Ligase
- Joins the Okazaki fragments together on the lagging strand to make a complete continuous strand.
📊 Comparison: Leading vs Lagging Strand
| Feature | Leading Strand | Lagging Strand |
|---|---|---|
| Direction relative to fork | Same as fork movement | Opposite to fork movement |
| Synthesis type | Continuous | Discontinuous (Okazaki fragments) |
| Enzyme needed to join fragments | No (polymerase alone) | Yes (DNA ligase) |
| Speed | Faster | Slower |
📌 Why 5′ → 3′ Only?
- DNA polymerase can add nucleotides only to the 3′ end of a growing strand.
- This chemical restriction causes one strand to be continuous and the other discontinuous.
🧠 Key Takeaways:
– DNA replication is semi-conservative: each new molecule has one old and one new strand.
– DNA polymerase builds new DNA only in the 5′ → 3′ direction.
– Leading strand is continuous; lagging strand is discontinuous and joined by DNA ligase.
– Accurate base pairing ensures genetic fidelity.
– DNA replication is semi-conservative: each new molecule has one old and one new strand.
– DNA polymerase builds new DNA only in the 5′ → 3′ direction.
– Leading strand is continuous; lagging strand is discontinuous and joined by DNA ligase.
– Accurate base pairing ensures genetic fidelity.
Structure of an RNA Molecule – Example: Messenger RNA (mRNA)
🌱 Overview
- RNA (Ribonucleic Acid) is a single-stranded nucleic acid made of nucleotides.
- mRNA carries genetic information from DNA in the nucleus to ribosomes in the cytoplasm for protein synthesis.
🧩 Components of mRNA Nucleotides
- Nitrogenous Base: Purines – Adenine (A), Guanine (G); Pyrimidines – Cytosine (C), Uracil (U) → replaces thymine found in DNA.
- Pentose Sugar: Ribose (contains one more oxygen atom than deoxyribose in DNA).
- Phosphate Group: Links nucleotides via phosphodiester bonds to form the sugar-phosphate backbone.
🔬 Structural Features of mRNA
| Feature | Description | Importance |
|---|---|---|
| Single-stranded | Not a double helix like DNA | Allows folding into shapes for function |
| Sequence of bases | Complementary to DNA template strand | Encodes amino acid sequence |
| 5′ cap (eukaryotes) | Modified guanine nucleotide at 5′ end | Protects mRNA & aids ribosome binding |
| Coding region | Series of codons (triplets of bases) | Each codon specifies an amino acid |
| 3′ poly-A tail (eukaryotes) | Chain of adenine nucleotides | Stabilises mRNA & regulates translation |
| Sugar-phosphate backbone | Formed by phosphodiester bonds | Gives molecule strength and stability |
📌 Key Differences Between mRNA and DNA
| Feature | mRNA | DNA |
|---|---|---|
| Strands | Single-stranded | Double-stranded helix |
| Sugar | Ribose | Deoxyribose |
| Bases | A, U, C, G | A, T, C, G |
| Stability | Less stable (short-lived) | More stable (long-term storage) |
| Location | Nucleus & cytoplasm | Nucleus (eukaryotes) |
🧠 Key Takeaways:
– mRNA is single-stranded, made of ribose nucleotides with bases A, U, C, G.
– Uracil replaces thymine, pairing with adenine during transcription.
– In eukaryotes, mRNA has a 5′ cap and 3′ poly-A tail for protection and translation efficiency.
– Acts as a messenger between DNA in the nucleus and ribosomes in the cytoplasm.
– mRNA is single-stranded, made of ribose nucleotides with bases A, U, C, G.
– Uracil replaces thymine, pairing with adenine during transcription.
– In eukaryotes, mRNA has a 5′ cap and 3′ poly-A tail for protection and translation efficiency.
– Acts as a messenger between DNA in the nucleus and ribosomes in the cytoplasm.