🧬 IB Biology SL - Theme A: Unity & Diversity
A1.2 - Nucleic Acids: The Molecules of Heredity
Understanding DNA and RNA structure, function, and the universal genetic code
🔬 Introduction: The Importance of Nucleic Acids
Essential Understanding:
Nucleic acids (DNA and RNA) are the information-carrying molecules in all living organisms. They store, transmit, and express genetic information, making them fundamental to life's continuity and diversity.
Nucleic acids are polymers made of nucleotide monomers. The two main types—DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)—work together to store genetic information and direct protein synthesis, which determines an organism's structure and function.
🎯 Key Functions of Nucleic Acids:
- Information storage: DNA stores genetic instructions (genome)
- Information transmission: DNA replication passes information to daughter cells
- Information expression: RNA transcribes and translates DNA into proteins
- Heredity: Genetic information passed from parents to offspring
- Evolution: Mutations in DNA create variation for natural selection
⚠️ IB Biology Context:
Understanding nucleic acid structure is essential for topics including gene expression, protein synthesis, cell division, genetics, and evolution. Master this foundation early!
🧱 Nucleotides: The Building Blocks
Definition:
A nucleotide is the monomer (basic unit) of nucleic acids. Nucleotides polymerize through condensation reactions to form DNA and RNA strands.
Structure of a Nucleotide
Three Components of Every Nucleotide:
- Pentose sugar (5-carbon sugar):
- Deoxyribose in DNA (lacks oxygen at 2' carbon)
- Ribose in RNA (has -OH group at 2' carbon)
- Phosphate group (PO₄³⁻):
- Negatively charged
- Attached to 5' carbon of sugar
- Forms backbone of nucleic acid through phosphodiester bonds
- Nitrogenous base:
- Attached to 1' carbon of sugar
- Contains nitrogen atoms
- Determines the specific nucleotide identity
📊 Generalized Nucleotide Structure
Phosphate (PO₄³⁻)
|
|
5'---Sugar---1'
|
|
Nitrogenous Base
Carbons numbered 1' through 5' (prime notation)
Phosphate on 5' carbon | Base on 1' carbon
Sugar Comparison: Ribose vs. Deoxyribose
| Feature | Ribose (RNA) | Deoxyribose (DNA) |
|---|---|---|
| Chemical Formula | C₅H₁₀O₅ | C₅H₁₀O₄ |
| Structure at 2' Carbon | -OH (hydroxyl group) | -H (hydrogen only) |
| Name Meaning | "Ribose" - full oxygenation | "Deoxy" = without oxygen |
| Stability | Less stable (reactive -OH) | More stable (less reactive) |
| Found In | RNA molecules | DNA molecules |
🔬 Sugar Structure Comparison
RIBOSE (RNA) DEOXYRIBOSE (DNA)
OH H
| |
5'---C---1' 5'---C---1'
| |
2' 2'
| |
OH OH
5' Phosphate---Sugar---Base
|
| (phosphodiester bond)
|
3' OH---Sugar---Base
|
| (phosphodiester bond)
|
Sugar---Base 5'
💡 IB Exam Tip:
Be able to draw and label a nucleotide showing all three components. Know the difference between ribose and deoxyribose—this comes up frequently on exams!
🔤 Nitrogenous Bases: The Genetic Alphabet
Overview:
There are five different nitrogenous bases in nucleic acids. The sequence of bases along a DNA or RNA strand encodes genetic information.
Two Categories of Bases
1. PURINES (Double-ring structure):
- Adenine (A): Found in both DNA and RNA
- Guanine (G): Found in both DNA and RNA
- Structure: Two fused rings (larger molecule)
- Mnemonic: "Pure As Gold" (Purines = A & G)
2. PYRIMIDINES (Single-ring structure):
- Cytosine (C): Found in both DNA and RNA
- Thymine (T): Found ONLY in DNA
- Uracil (U): Found ONLY in RNA (replaces thymine)
- Structure: Single six-membered ring (smaller molecule)
- Mnemonic: "CUT the Py" (Pyrimidines = C, U, T)
🧪 Chemical Structures of Nitrogenous Bases
PURINES (2 rings) PYRIMIDINES (1 ring)
Adenine (A) Cytosine (C)
Double ring Single ring
[Hexagon-Pentagon] [Hexagon]
Guanine (G) Thymine (T) - DNA only
Double ring Single ring
[Hexagon-Pentagon] [Hexagon with CH₃]
Uracil (U) - RNA only
Single ring
[Hexagon without CH₃]
Base Composition in DNA vs. RNA
| Nucleic Acid | Purines | Pyrimidines | Total Bases |
|---|---|---|---|
| DNA | Adenine (A), Guanine (G) | Cytosine (C), Thymine (T) | Four: A, G, C, T |
| RNA | Adenine (A), Guanine (G) | Cytosine (C), Uracil (U) | Four: A, G, C, U |
🎯 Key Difference:
DNA uses Thymine (T) while RNA uses Uracil (U). Both are pyrimidines that pair with adenine, but thymine has a methyl group (-CH₃) that uracil lacks.
Chargaff's Rules
Chargaff's Base Pairing Rules (DNA only):
- Rule 1: Amount of adenine (A) = Amount of thymine (T)
- Rule 2: Amount of guanine (G) = Amount of cytosine (C)
- Consequence: %A = %T and %G = %C in double-stranded DNA
- Total: %Purines (A + G) = %Pyrimidines (T + C)
- Significance: Provided evidence for base pairing in DNA structure
Example Calculation:
If a DNA molecule is 30% adenine (A), what percentage is each other base?
- A = 30%, therefore T = 30% (Chargaff's rule)
- A + T = 60%, therefore G + C = 40%
- G = C, so G = 20% and C = 20%
- Answer: A = 30%, T = 30%, G = 20%, C = 20%
🧬 DNA Structure: The Double Helix
Watson and Crick Model (1953):
James Watson and Francis Crick proposed the double helix structure of DNA based on X-ray crystallography data from Rosalind Franklin and Maurice Wilkins. This discovery revolutionized biology.
Key Features of DNA Structure
Structural Characteristics:
- Double-stranded: Two polynucleotide chains run alongside each other
- Antiparallel: Strands run in opposite directions (5'→3' and 3'→5')
- Helical shape: Strands twist around each other forming a helix
- Sugar-phosphate backbone: Forms the outside of the helix (hydrophilic)
- Bases inside: Nitrogenous bases point inward (hydrophobic)
- Complementary base pairing: A pairs with T; G pairs with C
- Hydrogen bonding: Bases held together by hydrogen bonds
- Major and minor grooves: Spaces between backbone spirals
🌀 DNA Double Helix Structure
5' ────P─S─P─S─P─S─P─S──── 3' (Strand 1: 5' to 3') │ │ │ │ │ │ │ │ A═T G≡C T═A C≡G (Base pairs with H-bonds) │ │ │ │ │ │ │ │ 3' ────S─P─S─P─S─P─S─P──── 5' (Strand 2: 3' to 5') S = Sugar (deoxyribose) P = Phosphate ═ = 2 hydrogen bonds (A-T) ≡ = 3 hydrogen bonds (G-C)
Note: Strands are ANTIPARALLEL (opposite directions)Helix makes one complete turn every 10 base pairs
Antiparallel Strands
What Does "Antiparallel" Mean?
- Definition: The two DNA strands run in opposite directions
- 5' to 3' direction: One strand oriented 5' carbon to 3' carbon
- 3' to 5' direction: Complementary strand runs 3' to 5'
- Phosphodiester bonds: Form in opposite directions on each strand
- Why important: DNA replication and transcription occur 5' → 3' only
Identifying 5' and 3' Ends:
- 5' end: Has free phosphate group on 5' carbon of sugar
- 3' end: Has free hydroxyl (-OH) group on 3' carbon of sugar
- By convention, DNA sequences written 5' → 3' direction
- Example: 5'-ATCG-3' (complementary: 3'-TAGC-5')
↕️ Antiparallel Orientation
Strand 1 (5' → 3') Strand 2 (3' → 5') 5' Phosphate 3' OH | | Sugar---A═══T---Sugar | | Phosphate Phosphate | | Sugar---T═══A---Sugar | | Phosphate Phosphate | | Sugar---C≡≡≡G---Sugar | | 3' OH 5' Phosphate
⚠️ Common IB Exam Error:
Students often forget to label strands as antiparallel. When drawing DNA, ALWAYS indicate 5' and 3' ends on both strands going in opposite directions!
Complementary Base Pairing
Base Pairing Rules:
- Adenine (A) pairs with Thymine (T): 2 hydrogen bonds (A=T)
- Guanine (G) pairs with Cytosine (C): 3 hydrogen bonds (G≡C)
- Complementarity: Base sequence of one strand determines the other
- Purine-Pyrimidine pairing: Large base pairs with small base (consistent width)
Why These Specific Pairs?
- Size complementarity: Purine + Pyrimidine = consistent helix width
- Hydrogen bonding: A-T has 2 H-bonds; G-C has 3 H-bonds
- Shape fit: Only these pairs have correct geometry to fit together
- G-C stronger: Three H-bonds make G-C pairs more stable than A-T pairs
- DNA stability: Higher %GC content = more stable DNA (higher melting temperature)
🔗 Hydrogen Bonding Between Base Pairs
ADENINE === THYMINE
(A) = = (T)
(2 hydrogen bonds)
Purine Pyrimidine
GUANINE ≡≡≡ CYTOSINE
(G) ≡ ≡ ≡ (C)
(3 hydrogen bonds)
Purine Pyrimidine
Practice: Determining Complementary Sequence
Given one DNA strand: 5'-ATCGGATC-3'
Complementary strand: 3'-TAGCCTAG-5'
Steps:
- Apply base pairing rules: A↔T, G↔C
- Write in antiparallel direction (opposite 5'/3' orientation)
- Check: Each A pairs with T, each G pairs with C
DNA Stability
Forces Stabilizing DNA Double Helix:
- Hydrogen bonds: Between complementary base pairs (weak individually, strong collectively)
- Base stacking: Van der Waals forces between adjacent bases
- Hydrophobic interactions: Bases shield from water in helix interior
- Covalent bonds: Phosphodiester bonds in sugar-phosphate backbone (very strong)
📜 RNA Structure: Single-Stranded Versatility
Overview:
RNA (ribonucleic acid) is typically single-stranded and more versatile than DNA. It plays multiple roles in gene expression and cellular regulation.
Key Features of RNA Structure
Structural Characteristics:
- Single-stranded: One polynucleotide chain (usually)
- Ribose sugar: Contains -OH group at 2' carbon
- Uracil instead of thymine: U pairs with A
- Shorter than DNA: Typically hundreds to thousands of nucleotides
- Can fold: Single strand can form secondary structures
- More reactive: Less stable than DNA due to 2'-OH group
- Temporary: Usually degraded after use
📏 RNA Structure (Single-Stranded)
5' Phosphate | Ribose---Adenine (A) | Phosphate | Ribose---Uracil (U) | Phosphate | Ribose---Guanine (G) | Phosphate | Ribose---Cytosine (C) | 3' OH (Can fold back on itself with base pairing)
DNA vs. RNA: Structural Comparison
| Feature | DNA | RNA |
|---|---|---|
| Sugar | Deoxyribose (no OH at 2') | Ribose (OH at 2') |
| Bases | Adenine, Guanine, Cytosine, Thymine | Adenine, Guanine, Cytosine, Uracil |
| Structure | Double-stranded helix | Single-stranded (can fold) |
| Length | Very long (millions-billions of nucleotides) | Shorter (hundreds-thousands) |
| Stability | Very stable | Less stable, easily degraded |
| Location | Nucleus (eukaryotes), nucleoid (prokaryotes) | Nucleus and cytoplasm |
| Function | Long-term information storage | Temporary information carrier, catalysis |
Types of RNA
Three Main Types (IB Biology Focus):
- mRNA (messenger RNA):
- Carries genetic information from DNA to ribosomes
- Template for protein synthesis
- Contains codons (3-nucleotide sequences)
- Single-stranded, linear structure
- tRNA (transfer RNA):
- Brings amino acids to ribosomes during translation
- Contains anticodon complementary to mRNA codon
- Cloverleaf secondary structure (3D: L-shaped)
- Each tRNA specific for one amino acid
- rRNA (ribosomal RNA):
- Structural and catalytic component of ribosomes
- Forms peptide bonds between amino acids
- Most abundant type of RNA in cells
- Combined with proteins to form ribosome subunits
🔄 Three Types of RNA
mRNA tRNA rRNA (Linear) (Cloverleaf) (Complex structure) 5'--AUG--CCC-- [Anticodon] [Part of ribosome] UAA--3' | | Amino acid Catalyzes peptide attachment bond formation site
💡 IB Tip:
Remember: RNA uses URACIL (U) instead of thymine. When transcribing DNA to RNA, replace all T's with U's!
🔢 Conservation of the Genetic Code
Universal Genetic Code:
The genetic code is the set of rules by which information encoded in genetic material (DNA/RNA) is translated into proteins. It is nearly universal across all life forms.
What is the Genetic Code?
Key Features of the Genetic Code:
- Triplet code: Three nucleotides (codon) code for one amino acid
- 64 possible codons: 4³ = 64 combinations of three bases
- 20 amino acids: Standard amino acids used in proteins
- Degenerate (redundant): Multiple codons can code for same amino acid
- Unambiguous: Each codon specifies only one amino acid
- Start codon: AUG (methionine) initiates translation
- Stop codons: UAA, UAG, UGA terminate translation
🧬 Genetic Code Table (Simplified)
Second Position U C A G ┌────────────────────────────────────────┐ U │ UUU-Phe UCU-Ser UAU-Tyr UGU-Cys │ U │ UUC-Phe UCC-Ser UAC-Tyr UGC-Cys │ First│ UUA-Leu UCA-Ser UAA-STOP UGA-STOP│ U │ UUG-Leu UCG-Ser UAG-STOP UGG-Trp │ ├────────────────────────────────────────┤ C │ CUU-Leu CCU-Pro CAU-His CGU-Arg │ C │ CUC-Leu CCC-Pro CAC-His CGC-Arg │ C │ CUA-Leu CCA-Pro CAA-Gln CGA-Arg │ C │ CUG-Leu CCG-Pro CAG-Gln CGG-Arg │ ├────────────────────────────────────────┤ A │ AUU-Ile ACU-Thr AAU-Asn AGU-Ser │ A │ AUC-Ile ACC-Thr AAC-Asn AGC-Ser │ A │ AUA-Ile ACA-Thr AAA-Lys AGA-Arg │ A │ AUG-Met* ACG-Thr AAG-Lys AGG-Arg │ ├────────────────────────────────────────┤ G │ GUU-Val GCU-Ala GAU-Asp GGU-Gly │ G │ GUC-Val GCC-Ala GAC-Asp GGC-Gly │ G │ GUA-Val GCA-Ala GAA-Glu GGA-Gly │ G │ GUG-Val GCG-Ala GAG-Glu GGG-Gly │ └────────────────────────────────────────┘ *AUG = Start codon (also codes for Methionine)
Why is the Genetic Code "Universal"?
Conservation Across Species:
- Same codons: Nearly identical code in bacteria, plants, animals, fungi
- AUG = start: All organisms use AUG as start codon
- Same stop codons: UAA, UAG, UGA universal stop signals
- Evidence for common ancestry: All life descended from common ancestor
- Minor exceptions: Some mitochondria and bacteria have slight variations
Implications of Universal Code:
- Genetic engineering: Human genes can be expressed in bacteria
- Insulin production: Bacteria produce human insulin using human DNA
- Evolutionary evidence: Supports common origin of all life
- Protein synthesis: Same mechanisms work across species
- Research applications: Model organisms (E. coli, yeast) relevant to humans
Redundancy (Degeneracy) of the Code
Why Multiple Codons per Amino Acid?
- 64 codons: Only 20 amino acids + 3 stop codons
- Extra codons: Multiple codons code for same amino acid
- Third base wobble: Third position of codon often variable
- Examples:
- Leucine: 6 different codons (UUA, UUG, CUU, CUC, CUA, CUG)
- Glycine: 4 codons (GGU, GGC, GGA, GGG)
- Methionine: 1 codon (AUG) - only one!
- Advantage: Protection against point mutations
📝 IB Exam Application:
You may need to use the genetic code table to translate mRNA sequences into amino acid sequences. Practice this skill—it appears frequently on Paper 2!
Practice Example
Question: Translate the following mRNA sequence:
5'-AUGUUCGAAUGA-3'
Click to reveal solution
📋 Summary: Nucleic Acids Comparison
| Property | DNA | RNA |
|---|---|---|
| Full Name | Deoxyribonucleic Acid | Ribonucleic Acid |
| Sugar | Deoxyribose | Ribose |
| Bases | A, G, C, T (Thymine) | A, G, C, U (Uracil) |
| Structure | Double helix (2 strands) | Single strand |
| Strand Orientation | Antiparallel | N/A (single strand) |
| Base Pairing | A-T (2 H-bonds), G-C (3 H-bonds) | Can pair with itself: A-U, G-C |
| Length | Very long (millions of bp) | Short to medium (100s-1000s) |
| Stability | Very stable | Less stable (2'-OH reactive) |
| Location | Nucleus, mitochondria, chloroplasts | Nucleus, cytoplasm, ribosomes |
| Function | Genetic information storage | Protein synthesis, regulation, catalysis |
🎓 Key Takeaways for IB Biology SL:
- Nucleotides are composed of sugar + phosphate + base
- DNA is double-stranded and antiparallel with complementary base pairing
- RNA is typically single-stranded and uses uracil instead of thymine
- The genetic code is nearly universal, supporting common ancestry
- Complementary base pairing enables DNA replication and transcription
- Understanding structure is essential for gene expression and inheritance
📝 IB-Style Practice Questions
Question 1 (2 marks):
State two differences between the structure of DNA and RNA.
Click to reveal answer
Question 2 (3 marks):
Explain what is meant by the term "antiparallel" in relation to DNA structure.
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Question 3 (4 marks):
If a sample of DNA contains 22% guanine, calculate the percentage of each of the other three bases.
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Question 4 (5 marks):
Outline the structure of a nucleotide and explain how nucleotides are linked together to form a polynucleotide.
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Question 5 (6 marks):
Explain the significance of complementary base pairing in DNA.
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