IB DP Biology: DNA replication, mutation and gene editing (DP Biology) – Revision Notes

These revision notes condense IB Diploma Programme Biology sections D1.1 (DNA replication) and D1.3 (Mutation and gene editing) from the IB Biology guide, first assessment 2025. For full explanations and worked examples, read the study guide. Statements D1.1.6 to D1.1.9 and D1.3.8 to D1.3.10 are HL only and are marked; the rest is SL and HL.

Test yourself with the practice set, then check the IB DP Biology hub, the printable checklist and the free 10-minute diagnostics.

Replication at a glance (D1.1.1 to D1.1.3)

• Replication produces exact copies: same base sequence.
• Needed so organisms can reproduce and so multicellular ones can grow and repair tissue.
• Semi-conservative: each new molecule = one original strand + one new strand.
• Accuracy comes from complementary base pairing: A-T, G-C, joined by hydrogen bonds. The template decides which base can enter.
• Helicase unwinds the helix by breaking hydrogen bonds between the strands.
• DNA polymerase builds the new strand by linking nucleotides that pair with the template.

Rounds of replication (n)	Total molecules (2ⁿ)	Molecules holding an original strand	Fraction
1	2	2	1
2	4	2	1/2
3	8	2	1/4
4	16	2	1/8

Method: fraction with an original strand = 2 ÷ 2ⁿ for a starting double helix.

PCR and gel electrophoresis (D1.1.4, D1.1.5)

Item	Role
Primers	Short single strands that bind to the ends of the target; give polymerase a 3’ end to extend
Taq polymerase	Heat-stable DNA polymerase from a thermophilic bacterium; survives the denaturing step
Free nucleotides	Building blocks for new strands
Denaturation (about 95 °C)	Separates strands
Annealing (about 55 to 60 °C)	Primers bind
Extension (about 72 °C)	New strands made

Ideal copies after n cycles = 2ⁿ.

Method: estimating fragment size from a gel

1. Measure distance moved from the well for each ladder band and the sample.
2. Plot log (size) against distance for the ladder, or use halving per fixed distance if the ladder shows it.
3. Read the sample size from the line.
4. Quote it with “about” and units (bp).

Key facts: DNA is negatively charged (phosphate groups), so it moves towards the positive electrode. Smaller fragments move further.

DNA profiling uses amplified variable markers. Uses: forensics, paternity. More markers = smaller chance of a false match; multiply the individual match probabilities for independent markers.

Detail of replication (HL only: D1.1.6 to D1.1.9)

Term	Meaning
5’ end	Free phosphate on carbon 5’ of the end nucleotide
3’ end	Free hydroxyl on carbon 3’ of the end nucleotide
Direction of synthesis	5’ to 3’ (polymerase adds the incoming 5’ phosphate to the 3’ end)
Leading strand	Continuous; one primer
Lagging strand	Discontinuous; Okazaki fragments; a primer for each

Prokaryotic enzyme	Function
Primase	Synthesises RNA primers
DNA polymerase III	Extends primers with DNA; proofreads
DNA polymerase I	Replaces RNA primers with DNA
DNA ligase	Joins fragments into a continuous strand

Proofreading: polymerase III removes a mismatched nucleotide at the 3’ terminal and inserts the correct one.

Method: replication time

1. Number of forks and the length each copies = genome length ÷ number of forks.
2. Time = length per fork ÷ speed.
3. Convert seconds to minutes.

Gene mutations (D1.3.1 to D1.3.3)

Mutation	Description	Typical effect
Substitution	One base replaced	Silent, missense or nonsense
Insertion	Base(s) added	Frameshift unless a multiple of three
Deletion	Base(s) lost	Frameshift unless a multiple of three

• SNP: a single-nucleotide difference at one position among individuals, from a substitution.
• Degeneracy of the code means a substitution may leave the amino acid unchanged.
• Frameshift: changes every codon downstream; the polypeptide is very likely non-functional.
• Large insertions or deletions can destroy function even in frame.

Method: classify a point mutation

1. Write the original and mutated codons.
2. Look up both amino acids.
3. Same amino acid: silent. Different: missense. Stop: nonsense.

Causes, randomness, consequences (D1.3.4 to D1.3.7)

• Causes: unrepaired errors in replication or repair; mutagens (chemical examples: nitrous acid; radiation: ultraviolet, X-rays, gamma rays).
• Random: can happen at any position; some bases mutate more often; no known natural mechanism for aiming a change at a base to alter a trait.
• Germ cells: mutation can be inherited and present in every cell of the offspring.
• Somatic cells: not inherited; can cause cancer.
• Source of variation: mutation creates new alleles; most harmful or neutral for the individual, but essential in the long term for evolution by natural selection.
• Nature of science: commercial genetic tests give risk information that needs expert interpretation.

Gene editing and conservation (HL only: D1.3.8 to D1.3.10)

• Knockout: make a gene inoperative, compare with normal organisms, infer function. Knockout libraries exist for some model species.
• CRISPR-Cas9: a guide RNA matches a target sequence; Cas9 cuts the DNA there; repair disables the gene or uses a supplied template to change it. A real use: a CRISPR-based treatment for sickle cell disease, authorised in 2023.
• Ethics: some uses must be resolved before use; regulation differs between countries, so there is an international effort to harmonise it.
• Conserved sequence: similar across a species or group. Highly conserved: similar over long evolutionary periods.
• Hypotheses: (1) function of the gene product restricts change, so selection removes variants; (2) a slower mutation rate in that region.

Worked reminders

Template to new strand. Template 3’ CCATG 5’ gives new strand 5’ GGTAC 3’. Pair each base, then state the direction of the new strand.

Frameshift check. mRNA 5’ AUG GAA GGC UAA 3’ codes Met-Glu-Gly-stop. Delete the first G of GAA: AUG AAG GCU AA reads Met-Lys-Ala, and the stop codon is lost. Delete the whole codon GAA instead: Met-Gly-stop, one amino acid fewer, same frame.

Reliability (nature of science). More markers in a DNA profile, or more repeat measurements in a knockout comparison, make a conclusion more reliable.

Must-know distinctions

Compare	Point of difference
Helicase vs polymerase	Helicase breaks hydrogen bonds; polymerase makes covalent bonds between nucleotides
Replication vs PCR	Replication uses helicase and primase in a cell; PCR uses heat and added primers
Silent vs missense	Same vs different amino acid
Missense vs nonsense	Different amino acid vs stop codon
Germ vs somatic	Inherited vs not inherited
Conserved vs highly conserved	Across species vs over long periods

Quick self-test

1. State what “semi-conservative” means.
2. A double helix replicates three times. What fraction of the molecules contain one of the original strands?
3. Ideal number of copies after 20 PCR cycles from one template?
4. Why is a heat-stable polymerase used in PCR?
5. Ladder bands: 600 bp at 10 mm and 300 bp at 20 mm (halving per 10 mm). Estimate a band at 25 mm.
6. Four independent markers have match chances 1 in 5, 1 in 9, 1 in 16 and 1 in 10. Combined chance?
7. A codon changes from UAU to UAA. Name the type of mutation and state the effect.
8. Explain why deleting one base is usually more damaging than deleting three.
9. HL only: a genome of 1.2 × 10⁶ bp is copied from one origin by two forks, each at 600 nucleotides per second. How long does replication take?
10. HL only: name the enzyme that seals gaps between Okazaki fragments, and the one that replaces RNA primers.
11. HL only: knockout plants form a mean of 6.8 lateral roots against 14.2 in normal plants. Calculate the percentage change.

Answers

1. Each new DNA molecule contains one original strand and one newly made strand.
2. 2 of 8 molecules = 1/4.
3. 2²⁰ = 1,048,576.
4. It is not denatured by the high-temperature denaturation step, so it keeps working through every cycle.
5. 5 mm past 300 bp: 300 × 2^(−0.5) = 212, so about 210 bp.
6. 5 × 9 × 16 × 10 = 1 in 7200.
7. Tyr codon becomes a stop codon: nonsense; the polypeptide ends early.
8. One base shifts the reading frame, changing every later codon; three bases remove one amino acid and leave the rest in frame.
9. Each fork copies 6 × 10⁵ bp; 600 000 ÷ 600 = 1000 s, about 17 min.
10. DNA ligase seals gaps; DNA polymerase I replaces primers.
11. (6.8 − 14.2) ÷ 14.2 × 100 = −52%.

Where marks are usually lost

• Writing “conservative” or “the strands separate and stay separate”.
• Mixing up bonds: helicase breaks hydrogen bonds, polymerase forms the sugar-phosphate backbone bonds.
• Omitting the role of primers in giving a 3’ end to extend.
• Saying DNA is positively charged, or that large fragments move furthest.
• Labelling a mutation “silent” without comparing the amino acids.
• Calling any insertion or deletion a frameshift; count the bases changed and test divisibility by three.
• HL: saying the lagging strand is made 3’ to 5’, or that it is “slower”.
• HL: describing CRISPR as only cutting; state that repair outcomes either disable or change the gene.
• Giving percentage change with the wrong denominator.

Official syllabus

IB Diploma Programme Biology guide, first assessment 2025, published by the International Baccalaureate Organization: sections D1.1 (DNA replication) and D1.3 (Mutation and gene editing).