Home / IBDP Biology 2025 SL&HL: A1.2 Nucleic acids Study Notes

IBDP Biology 2025 SL&HL: A1.2 Nucleic acids Study Notes

A1.2.1 – DNA as the Genetic Material of All Living Organisms

📌 Note:
All living organisms store genetic instructions in DNA, passed from cell to cell and generation to generation.

1. What is Genetic Material?

Genetic material stores hereditary information.

It can be copied and passed on from:

  • Cell to cell (during cell division)
  • Parent to offspring (during reproduction)

2. DNA: The Universal Genetic Material

  • DNA = Deoxyribonucleic Acid
  • Found in all living organisms.
  • It’s a large molecule made of repeating units called nucleotides.
  • DNA forms a polymer (a long chain).

3. Functions of Nucleic Acids

Nucleic AcidFull FormMain Role
DNADeoxyribonucleic acidStores genetic code for inheritance
RNARibonucleic acidHelps in protein synthesis (based on DNA)

DNA passes information between generations and carries instructions to make proteins via RNA.

4. What About RNA Viruses?

Some viruses (e.g. HIV, coronaviruses) use RNA instead of DNA.

However, viruses are not living because:

  • They are not made of cells
  • They can’t reproduce on their own (need a host cell)

So RNA viruses do not disprove the fact that all living organisms use DNA.

5. Universal Use of DNA = Common Ancestry

The fact that all life forms use DNA strongly supports the idea of a shared origin.
Scientists compare DNA sequences to:

  • Understand evolutionary relationships
  • Measure genetic similarity between species

A1.2.2 – Components of a Nucleotide

1. What is a Nucleotide?

  • A nucleotide is the basic building block (monomer) of nucleic acids like DNA and RNA
  • Nucleotides join together to form long chains of DNA or RNA

Each nucleotide consists of three distinct parts that work together to form the repeating unit of genetic molecules.

📌 Note:
Nucleotides = Phosphate + Sugar + Nitrogenous Base → form the core of DNA/RNA structure.

2. The Three Components of a Nucleotide

ComponentDescription
Phosphate groupA negatively charged group (contains phosphorus)
Pentose sugar5-carbon sugar: deoxyribose (DNA) or ribose (RNA)
Nitrogenous baseNitrogen-containing base (A, T, G, C, U)

3. Visual Representation (for Diagrams)

  • Circle = Phosphate
  • Pentagon = Sugar (pentose)
  • Rectangle = Nitrogenous base
  • Connected in the order: Phosphate → Sugar → Base
💡 Tip: This consistent structure allows nucleotides to form long, stable chains in DNA and RNA.

4. Sugar Structure – Carbon Numbering

  • The sugar ring contains 5 carbon atoms, labeled 1′ to 5′ (prime)
  • Numbering starts at the oxygen atom in the ring and moves clockwise
  • Phosphate group binds to the 5′ carbon, base binds to the 1′ carbon

A1.2.3 – Sugar – Phosphate Bonding and the Backbone of DNA & RNA

1. What is the Sugar-Phosphate Backbone?

  • It’s the strong structural framework of DNA and RNA strands.
  • Made of alternating phosphate and sugar units (from each nucleotide).
  • Called the “backbone” because it holds the strand together and maintains sequence order.

2. How is the Backbone Formed?

📌 Note:
The sugar–phosphate backbone gives DNA and RNA their structural stability and polarity (5′ to 3′).

Nucleotides are joined by covalent bonds between:


  • The 5′ phosphate group of one nucleotide
  • The 3′ carbon of the sugar on the next nucleotide

This process is a condensation reaction, which releases a molecule of water.

3. Directionality of the Strand

Nucleic acid strands run from 5′ to 3′ direction.
The backbone follows a repeated pattern:

🔁 Backbone: Phosphate – Sugar – Phosphate – Sugar …

This continuous covalent chain creates a strong and stable strand.

🔹 Key Terms

TermMeaning
BackboneThe sugar–phosphate chain that forms the structural framework of DNA/RNA
5′ to 3′ linkageDirection of bonding between phosphate and sugar in nucleotide chains
Condensation reactionA reaction that forms a bond and releases water as a byproduct

A1.2.4 – Nitrogenous Bases: The Code of Life

1️⃣ What Are Nitrogenous Bases?

Nucleotides contain a nitrogen-containing base. These bases form the genetic code.

BaseFound In
Adenine (A)DNA & RNA
Guanine (G)DNA & RNA
Cytosine (C)DNA & RNA
Thymine (T)DNA only
Uracil (U)RNA only

2️⃣ The Genetic Code

The sequence of these bases in a DNA or RNA molecule forms a genetic code.
Each triplet of bases (called a codon) codes for one amino acid.
This sequence ultimately determines the structure of proteins.

🧪Gene:

Gene = DNA Code for a Protein
A gene is a specific sequence of DNA bases that codes for the creation of a particular protein.

 

Example:
A DNA gene with the base sequence ATG–GCC–TGA will be translated into a chain of amino acids that form a specific protein.

A1.2.5 – RNA as a Polymer Formed by Condensation of Nucleotide Monomers

1️⃣ What is RNA Made Of?

RNA is a single-stranded polymer made up of nucleotide monomers.

Each RNA nucleotide contains:

  • A phosphate group (circle)
  • A ribose sugar (pentagon/hexagon)
  • A nitrogenous base (rectangle – A, U, C, G)
📌Note:
RNA = Ribose sugar + Phosphate group + Nitrogenous base (A, U, C, G)

2️⃣ Formation of RNA Polymer

RNA nucleotides join via a condensation reaction.
The 5′ phosphate of one nucleotide bonds with the 3′ carbon of the ribose on the next.

🔗 This forms a phosphodiester bond and releases water as a byproduct.

3️⃣ Structure of an RNA Strand

An RNA strand has a sugar–phosphate backbone with nitrogenous bases projecting outwards.
It has a defined 5′ → 3′ direction, which is essential for processes like transcription.

🧪 Visual Tip:
Represent an RNA nucleotide as:
🟡 Circle = Phosphate    🔷 Pentagon/Hexagon = Ribose    📦 Rectangle = Nitrogenous Base
Connect 5′ phosphate to 3′ carbon of the next sugar to show the bonding direction.

A1.2.6 – DNA as a Double Helix Made of Two Antiparallel Strands Linked by Hydrogen Bonds Between Complementary Base Pairs

1. DNA: A Double-Stranded Molecule

  • DNA (Deoxyribonucleic acid) consists of two long nucleotide chains that form a twisted, ladder-like double helix.
  • Each strand has a sugar–phosphate backbone with inward-facing nitrogenous bases.

2. Antiparallel Arrangement

– One DNA strand runs 5′ to 3′, the other 3′ to 5′
– This antiparallel nature is essential for:

  • Accurate base pairing
  • DNA replication by enzymes like DNA polymerase
  • Correct reading direction for enzyme function

3. Base Pairing and Hydrogen Bonds

The nitrogenous bases form specific pairs by hydrogen bonding:

  • Adenine (A) pairs with Thymine (T) → 2 hydrogen bonds
  • Guanine (G) pairs with Cytosine (C) → 3 hydrogen bonds

This is called complementary base pairing and it:

  • Ensures genetic consistency during DNA replication
  • Allows easy separation for replication or transcription

 

4. Importance of Hydrogen Bonding

Hydrogen bonds are individually weak, but collectively strong – just enough to stabilize DNA while allowing strand separation when needed.

5. Summary of Key Features

FeatureDescription
Double helixTwo nucleotide strands twisted around each other
Antiparallel strandsOne strand runs 5′→3′, the other 3′→5′
Complementary base pairingA–T and G–C pairing with hydrogen bonds
Hydrogen bondsHold strands together, allow easy separation
Sugar–phosphate backboneGives stability and direction to the strands
Biological significanceEnsures accurate copying and storage of DNA

🔍 Why It Matters

Without antiparallel orientation, DNA polymerase cannot function properly.
Without complementary base pairing, DNA replication would be error-prone.
Without hydrogen bonds, the double helix would be too unstable to preserve genetic code.
 

A1.2.7 – Differences Between DNA and RNA

1. Common Features of DNA & RNA

  • Both are nucleic acids
  • Both are polymers of nucleotides
  • Both have a sugar–phosphate backbone
  • Both store and carry genetic information
  • Both are formed via condensation reactions
📌 Note:
DNA and RNA differ in structure, function, and stability, but share the same basic building blocks.

2. Key Differences Between DNA and RNA

FeatureDNARNA
Full nameDeoxyribonucleic acidRibonucleic acid
StrandsDouble-stranded (helix)Single-stranded
SugarDeoxyriboseRibose
BasesA, T, G, CA, U, G, C
Base pairingA–T, C–GA–U, C–G
StabilityMore stableLess stable
FunctionsStores genetic codeProtein synthesis roles

3. Structural Difference in Sugars

Ribose has an –OH group on the 2′ carbon, while deoxyribose has just a –H (missing one oxygen).

➡️ Students should sketch both sugars showing the extra –OH group on ribose.

4. Location in Cells

FeatureDNARNA
Eukaryotic cellsNucleus, mitochondria, chloroplastsNucleus, cytoplasm, ribosomes, rough ER
Prokaryotic cellsCytoplasm (nucleoid region)Cytoplasm (free or at ribosomes)

5. Examples of Nucleic Acids

  • DNA: Human genome, bacterial chromosomes, mitochondrial DNA
  • RNA types:
    • mRNA – Messenger RNA (carries genetic message)
    • tRNA – Transfer RNA (helps assemble proteins)
    • rRNA – Ribosomal RNA (forms ribosomes)

📘 Summary Table

CriteriaDNARNA
Strand TypeDoubleSingle
SugarDeoxyriboseRibose
BasesA, T, G, CA, U, G, C
Base PairingA–T, C–GA–U, C–G
LocationNucleus, mitochondria, chloroplastsNucleus, cytoplasm, ribosome
FunctionStores hereditary infoProtein synthesis

A1.2.8 – Role of Complementary Base Pairing in Genetic Replication and Expression

1. What is Complementary Base Pairing?

  • Adenine (A) pairs with Thymine (T) in DNA
  • Adenine (A) pairs with Uracil (U) in RNA
  • Cytosine (C) pairs with Guanine (G)
  • This occurs due to hydrogen bonding between bases

2. Role in DNA Replication

  • Before cell division, DNA must replicate exactly
  • The two strands unzip by breaking hydrogen bonds
  • Each original strand acts as a template
  • Free nucleotides pair up using base-pairing rules:
    • A → T
    • C → G
  • Result: New strands are exact copies → ensures genetic stability

3. Role in Transcription (DNA → mRNA)

  • One DNA strand serves as the template
  • RNA bases pair with DNA to form mRNA:
    • A (DNA) → U (RNA)
    • T (DNA) → A (RNA)
    • C (DNA) → G (RNA)
    • G (DNA) → C (RNA)
  • This produces a correct mRNA strand ready for protein synthesis

4. Role in Translation (mRNA → Protein)

  • mRNA codons (triplets) are read by the ribosome
  • Each codon pairs with a complementary anticodon on tRNA
  • tRNA brings specific amino acids to the ribosome
  • Base pairing ensures correct amino acid order → proper protein structure

5. Summary of Roles

ProcessHow Complementary Base Pairing Helps
ReplicationEnsures accurate DNA copying for cell division
TranscriptionBuilds the correct mRNA strand from DNA template
TranslationMatches tRNA anticodons to mRNA codons to assemble proteins

Why It Matters:
Without complementary base pairing:

  • DNA wouldn’t replicate accurately → mutations
  • mRNA could carry incorrect instructions
  • Proteins might form incorrectly → malfunctioning cells

It is the foundation for genetic fidelity, heredity, and gene expression.

A1.2.9 – Diversity of DNA Base Sequences and the Limitless Capacity of DNA for Storing Information

1. DNA is a Universal Information Storage Molecule

DNA uses four bases – A, T, C, and G – to encode genetic instructions.

  • The order of bases forms the genetic code
  • Each unique sequence → a unique protein-coding message
Key Idea:
Four bases can be arranged in countless sequences, allowing DNA to store massive amounts of information.

2. Enormous Diversity Comes from Sequence and Length

  • 4² = 16 possible 2-base sequences
  • 4³ = 64 possible codons (triplets)
  • 4ⁿ sequences possible for any length “n”
  • 100-base DNA → more than 1.6 × 10⁶⁰ possible combinations
  • Longer DNA molecules = virtually infinite storage potential

3. Economy of Storage

DNA stores huge amounts of data in a compact space:

  • Each cell contains ~3 billion base pairs
  • Total DNA in one cell spans ~2 meters
  • All packed inside a tiny nucleus (≈ 6 µm)
📌Note:
DNA is incredibly efficient – it stores complex data in tiny spaces using just 4 bases!

4. DNA is Digital and Durable

  • Functions like a biological hard drive
  • Uses 4 chemical “letters”
  • Linear structure → easy to copy and transmit
  • Used in synthetic biology to store real-world data (texts, images, software!)

5. Biological Significance

  • Allows for huge genetic variation among species
  • Every individual has a unique DNA sequence
  • Supports countless combinations of genes and proteins
  • Despite sequence differences, all organisms share the same 4-base system

🔹 Summary Table

ConceptExplanation
Base SequenceOrder of A, T, G, C determines genetic code
Sequence LengthLonger sequences = more possible combinations
Storage PotentialEssentially limitless with just 4 bases
Biological OutcomeHuge genetic diversity and individuality

            

A1.2.10 – Conservation of the Genetic Code Across All Life Forms as Evidence of Universal Common Ancestry

1. What is the Genetic Code?

The genetic code is a system of rules for translating the base sequence in DNA or mRNA into a chain of amino acids (protein).

  • It uses triplets of bases called codons
  • Each codon codes for a specific amino acid or a stop signal

2. What Does ‘Universal Genetic Code’ Mean?

“Universal” means all living organisms use the same codon – amino acid mapping.

  • Example: AUG codes for methionine in all life forms – bacteria, plants, humans
  • Genetic code hasn’t changed through evolution
Key Idea:
The same codons produce the same amino acids in all organisms – a shared biological “language”.

3. Evidence for Universal Common Ancestry

  • All life shares the same genetic code logic
  • Strong evidence that life evolved from a common ancestor
  • Genetic code has been conserved for billions of years

4. Why It’s Important

The universality of the code allows scientists to:

  • Compare genes between species
  • Use bacteria to express human proteins (e.g., insulin)
  • Support the theory of evolution via molecular evidence
📌 Note:
The genetic code is like a global language – used identically in every known organism on Earth.

5. Summary Points

ConceptDetails
Genetic codeTriplet codons coding for amino acids
UniversalitySame codons used across all life
Evolutionary linkShared code = shared ancestry
ApplicationBiotech, gene transfer, evolutionary research

Additional Higher Level

 A1.2.11 – Directionality of RNA and DNA

1. What Does Directionality Mean in DNA/RNA?

Nucleic acids have two chemically distinct ends:

  • 5′ (five-prime): Has a phosphate group on the 5th carbon of the sugar
  • 3′ (three-prime): Has a hydroxyl group (-OH) on the 3rd carbon
💡 Key Insight:
The strand “grows” in the 5′ to 3′ direction – new nucleotides are always added at the 3′ end.

2. Antiparallel Nature of DNA

  • DNA has two strands running in opposite directions
  • One runs 5′ → 3′, the other 3′ → 5′
  • This is critical for correct base pairing, replication, and enzyme action

3. Importance in Replication

DNA polymerase can only add nucleotides to the 3′ end of a strand.

  • So DNA is synthesized in the 5′ to 3′ direction
  • Leads to:
    • Leading strand: made continuously
    • Lagging strand: made in fragments (Okazaki fragments)

4. Importance in Transcription

  • RNA polymerase reads the DNA template strand from 3′ to 5′
  • It builds mRNA in the 5′ to 3′ direction
  • This ensures the mRNA is complementary and properly oriented

5. Importance in Translation

  • Ribosomes read mRNA in the 5′ to 3′ direction
  • Each codon (3 bases) corresponds to one amino acid
  • This ensures correct reading frame and protein sequence

6. Quick Recap Table

ProcessEnzyme ReadsNew Strand Made
ReplicationDNA (3′ → 5′)DNA (5′ → 3′)
TranscriptionDNA template (3′ → 5′)mRNA (5′ → 3′)
TranslationmRNA (5′ → 3′)Polypeptide (amino acid chain)

🔍 Why It Matters
Directionality ensures:

  • Correct enzyme function and binding
  • Accurate gene expression
  • Proper protein synthesis

Even small directional mistakes can result in mutations or cellular malfunction.

A1.2.12 – Purine-to-Pyrimidine Bonding as a Component of DNA Helix Stability

1. What Are Purines and Pyrimidines?

DNA bases are grouped based on their structure:

GroupStructureBases
PurinesDouble-ringAdenine (A), Guanine (G)
PyrimidinesSingle-ringCytosine (C), Thymine (T), Uracil (U)

2. Base Pairing: Purine–Pyrimidine Rule

Each base pair in DNA = one purine + one pyrimidine, keeping the helix width consistent:

PairType# Hydrogen Bonds
A–TPurine–Pyrimidine2
C–GPurine–Pyrimidine3

3. Why Is Purine–Pyrimidine Pairing Important?

  • Equal Width: Maintains uniform shape of DNA helix
  • Hydrogen Bonds:
    • A–T = 2 H-bonds → stable but easy to unzip
    • C–G = 3 H-bonds → stronger, more heat resistant
  • Ensures DNA stability and accurate replication

🔍 Quick Tips for Identifying Bases:

  • 2 rings + 2 H-bonds → Adenine
  • 2 rings + 3 H-bonds → Guanine
  • 1 ring + 2 H-bonds → Thymine
  • 1 ring + 3 H-bonds → Cytosine

4. RNA Note

In RNA, Uracil (U) replaces Thymine (T)
→ A–U forms 2 hydrogen bonds

✅ Summary:
DNA base pairing follows a purine-to-pyrimidine rule
This provides structural consistency and double helix stability
Hydrogen bonds and consistent spacing are vital for DNA’s biological function

A1.2.13 – Structure of a Nucleosome

1. What Is a Nucleosome?

A nucleosome is the fundamental unit of DNA packaging in eukaryotic cells. It compacts long DNA strands while keeping them accessible for gene expression.

2. Components of a Nucleosome

ComponentDescription
Histone octamerCore of 8 histone proteins (2 each of H2A, H2B, H3, H4)
DNA~146 base pairs wrap around the histone core (2 loops)
Linker DNAStretch of DNA between nucleosomes
Histone H1Binds outside the core to stabilize and compact chromatin

3. Step-by-Step DNA Packaging

  • DNA Double Helix: The basic DNA strand
  • Nucleosome Formation: DNA wraps around histone octamer
  • “Beads-on-a-string”: Nucleosomes linked by linker DNA (interphase)
  • Chromatin Fiber: Nucleosomes coil into 30 nm fibers
  • Supercoiling: Chromatin twists into chromosomes (mitosis/meiosis)

4. Why Are Nucleosomes Important?

  • Compaction: Fits large genomes into small nuclei
  • Regulation: Controls access to genes for transcription
  • Protection: Prevents DNA damage and maintains integrity

5. Visualization Tip

In molecular diagrams:

  • 2 loops of DNA wrapped around the histone octamer
  • H1 protein sits outside securing the structure
  • Linker DNA connects adjacent nucleosomes
✅ Summary:
A nucleosome = DNA wrapped around a histone octamer, stabilized by H1 and linker DNA.
It is the first level of chromatin organization and is vital for packaging, gene regulation, and chromosome structure.

A1.2.14 – Evidence from the Hershey-Chase Experiment for DNA as the Genetic Material

🔍 Background:

Before 1952, scientists were uncertain whether DNA or protein carried genetic information. Both were present in cells and seemed likely candidates.

Experimental question: Is DNA or protein the molecule responsible for heredity?

🦠 Organisms Used

  • Bacteriophages – viruses that infect bacteria
  • Escherichia coli (E. coli) – bacterial host cells

🧬 Key Idea of the Experiment

Hershey and Chase used radioactive isotopes to label:

  • DNA with phosphorus-32 (32P) – because DNA contains phosphorus
  • Protein with sulfur-35 (35S) – because proteins contain sulfur

⚗️ Step-by-Step Procedure

  • Labeling: Phages were grown in media with either 32P or 35S
  • DNA was labeled with 32P; protein with 35S
  • Infection: Radioactive phages infected non-radioactive bacteria
  • Blending: Agitation separated phage coats from bacterial cells
  • Centrifugation: Heavier bacteria formed pellet; lighter phage coats remained in supernatant
  • Results: 32P was found in pellet (inside bacteria), 35S in supernatant (outside)
📌 Conclusion:
DNA, not protein, entered the bacteria and directed the production of new phages.
This provided strong evidence that DNA is the genetic material.

⚙️ Role of Technology (Nature of Science)

The use of radioisotopes was essential. Availability after WWII allowed scientists to track molecules precisely.
This experiment is a prime example of how new technology can enable scientific breakthroughs.

🧪 Radioisotopes in Biology

  • Radioactive isotopes like 32P and 35S act as tracers
  • They emit detectable radiation, helping scientists follow molecular pathways
  • Used today in DNA/RNA studies, metabolism research, and medical imaging
✅ Summary Points:
The Hershey–Chase experiment (1952) proved that DNA is the molecule of heredity
Used radioactive labels to distinguish DNA and protein
Only DNA entered bacterial cells and passed on instructions
Shifted scientific consensus toward DNA as the universal genetic material

 

A1.2.15 – Chargaff’s Data on Base Ratios Across Life Forms

📊 What Did Chargaff Discover?

Erwin Chargaff analyzed DNA samples from various species and made a critical observation:

  • Adenine (A)Thymine (T)
  • Guanine (G)Cytosine (C)
  • Thus, Purines (A, G) always equal Pyrimidines (T, C)

Although the overall percentage of each base varied between species, the ratio of A:T and G:C stayed close to 1:1.

📉 Falsification of the Tetranucleotide Hypothesis

🧪 Old Hypothesis:
The tetranucleotide hypothesis claimed that DNA was composed of repeating, equal amounts of the four bases — A = T = G = C.

Chargaff’s data showed this was false:

  • Base composition differed among species
  • But A:T and G:C ratios were always 1:1

Falsifiability Principle (Nature of Science)

  • Science advances not by proving ideas, but by disproving incorrect ones.
  • Chargaff’s evidence falsified the tetranucleotide model and cleared the path for more accurate models like the DNA double helix.

🧠 Induction vs. Falsification

  • Induction: Generalizing from patterns (e.g., equal base ratios)
  • Falsification: Actively disproving false models
  • Chargaff’s work supported falsifiability as a stronger scientific method

🧬 How Did It Help Watson & Crick?

Though Chargaff didn’t suggest base pairing himself, Watson and Crick used his data to understand:

  • A pairs with T, G pairs with C
  • This led to their model of the double helix with a uniform width and stable hydrogen bonding
✅ Summary Points:
Chargaff discovered A:T ≈ 1 and G:C ≈ 1 in all species
Disproved the old tetranucleotide model (A = T = C = G)
Helped establish the base-pairing principle
Demonstrates how falsification drives scientific progress

 

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