DNA Structure
The Double Helix Blueprint🧬 The Master Blueprint
Deoxyribonucleic acid (DNA) carries all the genetic instructions needed to build, run, and reproduce every living organism. It is found in the nucleus of every cell (in the chromosomes) and also in mitochondria and chloroplasts. Its structure — the famous double helix — was described by Watson and Crick in 1953, using X-ray crystallography data from Rosalind Franklin.
Building Block
The Nucleotide — DNA's LEGO Brick
Every DNA molecule is built from millions of nucleotides. Know the three components.
🧱 Three Components of a Nucleotide
- Deoxyribose sugar — 5-carbon (pentose) sugar; gives DNA its name (deoxy = missing one oxygen compared to ribose)
- Phosphate group — forms the backbone; links nucleotides together via phosphodiester bonds
- Nitrogenous base — one of four options (A, T, G, C); carries the genetic information
🔗 How Nucleotides Join
- Nucleotides join end-to-end via phosphodiester bonds between the sugar of one and the phosphate of the next
- This forms the sugar-phosphate backbone — the "sides" of the ladder
- The two strands run antiparallel — one runs 5' to 3', the other 3' to 5'
- The bases pair across the middle — "rungs" of the ladder
The Four DNA Bases — Chargaff's Rules
A
Adenine
Pairs with: T
Purine — 2 H bonds
T
Thymine
Pairs with: A
Pyrimidine — 2 H bonds
G
Guanine
Pairs with: C
Purine — 3 H bonds
C
Cytosine
Pairs with: G
Pyrimidine — 3 H bonds
⚠️ Exam Watch — Chargaff's Rules
A always pairs with T (2 hydrogen bonds). G always pairs with C (3 hydrogen bonds). This means: in any DNA molecule, %A = %T and %G = %C. Also: purines (A, G) always pair with pyrimidines (T, C). G-C pairs are stronger than A-T pairs (3 vs 2 H bonds). If given %G = 20%, then %C = 20%, and %A + %T = 60%, so %A = %T = 30%.
Double Helix Structure
The Twisted Ladder
Two antiparallel strands wound around each other. Know every level of this structure.
🏗️ Structural Features
- Two polynucleotide strands wound in a right-handed helix
- Sugar-phosphate backbone on the outside (hydrophilic)
- Bases on the inside, pointing toward each other
- Strands held together by hydrogen bonds between complementary bases
- Strands are antiparallel: one runs 5'→3', other runs 3'→5'
- Full twist every 10 base pairs; ~2nm diameter
📦 Packaging in the Nucleus
- DNA is extremely long — human genome = ~3 billion base pairs
- DNA wraps around histone proteins → nucleosome
- Nucleosomes coil and fold → chromatin fibre
- Chromatin condenses → chromosome (visible during cell division)
- Each human cell contains ~2 metres of DNA packed into a nucleus ~6 micrometres wide
📌 Levels of DNA Organisation
DNA double helix → wraps around histones (nucleosome) → coils into chromatin → condenses into chromosomes. This packaging reduces a 2-metre molecule to fit inside a microscopic nucleus. Chromosomes are only visible as distinct structures during cell division — during interphase, DNA is unwound as chromatin to allow transcription.
DNA Replication
Copying the Blueprint🔄 Semi-Conservative Replication
Before a cell divides, it must copy its entire DNA so each daughter cell gets a complete set of genetic instructions. This process — DNA replication — is described as semi-conservative because each new DNA molecule consists of one original (template) strand and one newly synthesised strand. It occurs during the S phase of the cell cycle, in the nucleus.
The Replication Steps
1
Unwinding — the enzyme helicase breaks the hydrogen bonds between base pairs, unzipping the double helix and separating the two strands at the replication fork. This creates two template strands.
2
Primer attachment — a short RNA primer binds to each template strand to provide a starting point for DNA synthesis. DNA polymerase cannot start from scratch — it can only add nucleotides to an existing strand.
3
New strand synthesis — DNA polymerase reads each template strand (3'→5') and adds complementary nucleotides (A-T, G-C) to build the new strand in the 5'→3' direction. Free nucleotides are added according to complementary base pairing rules.
4
Proofreading — DNA polymerase also proofreads as it goes, detecting and correcting mismatched base pairs. This gives replication an extraordinary accuracy of approximately 1 error per billion base pairs.
5
Result — two identical double-stranded DNA molecules, each containing one original strand and one new strand. This is semi-conservative replication.
| Enzyme | Role in Replication |
|---|---|
| Helicase | Unwinds and separates the two DNA strands by breaking hydrogen bonds between base pairs |
| DNA Polymerase | Adds new complementary nucleotides to the template strand; builds the new strand 5'→3'; also proofreads |
| Primase | Synthesises short RNA primers to provide a starting point for DNA polymerase |
| Ligase | Joins (seals) fragments of DNA together; seals the sugar-phosphate backbone |
⚠️ Exam Watch — Semi-Conservative Evidence
The Meselson-Stahl experiment (1958) proved semi-conservative replication using heavy nitrogen (¹⁵N) and light nitrogen (¹⁴N). Bacteria grown in ¹⁵N had heavy DNA. Transferred to ¹⁴N medium and allowed to replicate once — all DNA was intermediate density (one heavy, one light strand). Replicated again — half intermediate, half light. This pattern only fits semi-conservative replication, ruling out conservative and dispersive models.
RNA Types
The Working Copies📋 RNA — The Messenger Between Blueprint and Factory
Ribonucleic acid (RNA) is the working copy of the DNA blueprint. DNA stays safely in the nucleus; RNA carries the instructions out to the ribosomes where proteins are made. There are three main types of RNA, each with a specific role in protein synthesis. All three are made by transcription from a DNA template.
Type 1
mRNA — Messenger RNA
Carries the genetic message from nucleus to ribosome. The delivery driver.
⚙️ Structure & Function
- Single-stranded RNA molecule
- Made during transcription in the nucleus — a copy of one gene from DNA
- Carries the genetic code as a sequence of codons (triplets of bases)
- Travels from nucleus to ribosome in the cytoplasm
- Read by the ribosome during translation to build a protein
- Relatively short-lived — degraded after use
🔤 Codons
- Each codon = 3 consecutive bases on mRNA
- Each codon codes for one specific amino acid
- 64 possible codons (4³) code for only 20 amino acids — the code is degenerate (multiple codons per amino acid)
- Start codon: AUG (methionine) — signals where translation begins
- Stop codons: UAA, UAG, UGA — signal where translation ends (no amino acid)
Type 2
tRNA — Transfer RNA
Carries amino acids to the ribosome. The delivery truck that brings the correct building material.
⚙️ Structure & Function
- Small, clover-leaf shaped RNA molecule
- Has an anticodon — 3 bases that are complementary to a specific mRNA codon
- Has an attachment site at the 3' end for a specific amino acid
- Each tRNA carries only one specific amino acid — there is a different tRNA for each codon
- Brings the correct amino acid to the ribosome during translation
🎯 Anticodon Matching
- The tRNA anticodon pairs with the complementary mRNA codon at the ribosome
- Example: mRNA codon AUG → tRNA anticodon UAC
- This ensures the correct amino acid is added at each position
- The specificity of anticodon-codon pairing is what translates the genetic code accurately into a protein sequence
Type 3
rRNA — Ribosomal RNA
Forms the ribosome structure itself. The factory building, not just a worker.
⚙️ Structure & Function
- Most abundant type of RNA in the cell
- Together with ribosomal proteins, forms the ribosome
- Ribosome has two subunits: large and small — both contain rRNA
- The ribosome is the molecular machine that reads mRNA and assembles proteins
- rRNA plays both structural AND catalytic roles in translation
🔧 Ribosome Structure
- Small subunit — reads (decodes) the mRNA
- Large subunit — catalyses peptide bond formation between amino acids
- Ribosomes can be free in cytoplasm (soluble proteins) or bound to rough ER (secreted or membrane proteins)
- Multiple ribosomes can translate one mRNA simultaneously (polyribosome/polysome)
DNA vs RNA
Blueprint vs Working Copy⚖️ Same Language, Different Purpose
DNA and RNA are both nucleic acids built from nucleotides — but they differ in structure, stability, location, and function. Understanding these differences is essential for understanding both replication and protein synthesis, and is a guaranteed comparison question in any Life Sciences exam.
| Feature | DNA | RNA |
|---|---|---|
| Full name | Deoxyribonucleic acid | Ribonucleic acid |
| Sugar | Deoxyribose (missing one -OH group) | Ribose (has -OH group at 2' carbon) |
| Strands | Double-stranded (double helix) | Single-stranded |
| Bases | Adenine, Thymine, Guanine, Cytosine (A, T, G, C) | Adenine, Uracil, Guanine, Cytosine (A, U, G, C) — Uracil replaces Thymine |
| Base pairing | A-T and G-C | A-U and G-C (in double-stranded regions) |
| Location | Nucleus (also mitochondria, chloroplasts) | Nucleus and cytoplasm |
| Stability | Very stable — long-term storage | Relatively unstable — short-lived |
| Function | Stores and transmits genetic information | Carries and expresses genetic instructions (protein synthesis) |
| Amount in cell | Constant in all cells of an organism | Varies — more in cells actively making proteins |
| Types | One type | Three types: mRNA, tRNA, rRNA |
⚠️ The Single Most Tested Difference
The base Thymine (T) is found in DNA only. Uracil (U) is found in RNA only. If an exam question shows a sequence with U — it is RNA. If it shows T — it is DNA. Also: DNA has deoxyribose sugar (no -OH at 2' carbon); RNA has ribose sugar (has -OH at 2' carbon). This makes DNA more chemically stable — which is why DNA is used for long-term storage and RNA is used for short-term messaging.
🎯 Blueprint Inspection
Eight questions on DNA, RNA, and replication.
Question 1 of 8
A DNA sample is analysed and found to contain 22% adenine. What percentage of the bases are guanine?
Question 2 of 8
Which enzyme is responsible for UNWINDING the DNA double helix during replication?
Question 3 of 8
What is meant by "semi-conservative" DNA replication?
Question 4 of 8
Which base is found in RNA but NOT in DNA?
Question 5 of 8
What is the function of tRNA in protein synthesis?
Question 6 of 8
A DNA template strand reads 3'-TACGCAATT-5'. What is the complementary DNA strand (written 5' to 3')?
Question 7 of 8
Why is DNA more stable than RNA as a long-term information storage molecule?
Question 8 of 8
The genetic code is described as "degenerate." What does this mean?