Pearson Edexcel International A Level Biology: Decomposition, PCR, Electrophoresis and Forensic Biology (YBI11) – Revision Notes

Quick recall for the Pearson Edexcel International Advanced Subsidiary/Advanced Level Biology specification (YBI11), Issue 2, statements 6.16 to 6.20 in Topic 6. This topic is in Unit 4, the International A2 (IA2) part of the course. For full explanations read the study guide. Test yourself with the practice questions, use the Edexcel A Level Biology hub and the printable checklist, and find gaps with the free 10-minute diagnostics.

Key terms

Term	Meaning
Saprotroph	Bacterium or fungus that feeds on dead organic matter by extracellular digestion
Detritivore	Animal that eats dead material and fragments it (not a microorganism)
Primer	Short single-stranded DNA that anneals to the end of the target and starts copying
Taq polymerase	Heat-stable DNA polymerase from Thermus aquaticus
Thermocycler	Machine that repeats the temperature cycle automatically
Restriction enzyme	Enzyme that cuts DNA at a specific base sequence
DNA ladder	Mixture of fragments of known length run alongside samples
STR	Short tandem repeat: a short sequence repeated, with repeat number varying between people
Locus	Position of a gene or marker on a chromosome
Rigor mortis	Stiffening of muscles after death because no ATP is available

6.16 Decomposition and carbon recycling

Method in steps for how a saprotroph decomposes dead matter:

1. Secrete enzymes (proteases, lipases, carbohydrases) onto the material.
2. Large molecules are hydrolysed to small soluble molecules.
3. The products are absorbed.
4. Some are used for growth; some are respired, releasing carbon dioxide.

Carbon cycle links:

• Photosynthesis moves carbon from carbon dioxide into organic compounds.
• Feeding moves it along food chains.
• Respiration (including by saprotrophs) returns carbon dioxide to the air.
• Burial without full decomposition leads to fossil fuels; combustion returns the carbon dioxide.

Speed of decomposition rises with warmth, moisture, oxygen and near-neutral pH. Cold, dry, acidic or waterlogged conditions slow it, so organic matter such as peat accumulates.

Worked reminder: leaf litter of 40.0 g falls to 34.0 g in 30 days.

• Loss = 6.0 g, which is 6.0 / 40.0 × 100 = 15.0%
• Rate = 6.0 / 30 = 0.20 g per day

6.17 PCR

Component	Role
Template DNA	Contains the target sequence
Two primers	Anneal to opposite ends of the target and give the polymerase a start point
Free nucleotides	Raw material for new strands
Taq polymerase	Builds new strands without being denatured at about 95 °C
Buffer and magnesium ions	Keep conditions suitable for the enzyme

Cycle: denature (about 95 °C, strands separate) then anneal (about 50 to 65 °C, primers bind) then extend (about 72 °C, polymerase adds nucleotides). Repeat.

Copies after n cycles: starting number × 2ⁿ (idealised).

Worked reminder: how many cycles turn 10 target molecules into more than one million?

• After 16 cycles: 10 × 65 536 = 655 360, too few.
• After 17 cycles: 10 × 131 072 = 1 310 720.
• 17 cycles.

Uses: amplifying tiny samples for DNA profiling, with contamination as the main risk.

6.18 Gel electrophoresis

Method in steps:

1. Prepare an agarose gel in buffer.
2. Load samples and a DNA ladder into wells at the negative end.
3. Apply a current. Negatively charged DNA moves towards the positive electrode.
4. Shorter fragments travel further through the mesh.
5. Stain or label the DNA and view under UV light or by fluorescence.
6. Compare each band with the ladder.

Rule: distance moved changes in a roughly straight line with log (length), not with length.

Worked reminder: a ladder shows 6000 bp at 8 mm, 3000 bp at 16 mm, 1500 bp at 24 mm, 750 bp at 32 mm (8 mm per halving). A fragment ran 20 mm.

• 20 mm is 4 mm past 3000 bp, half a halving step.
• Length = 3000 × 2^(−4/8) = 3000 × 0.707 = 2121
• About 2100 bp.

6.19 DNA profiling

Aspect	Points to remember
What is compared	Number of repeats at several STR loci in non-coding DNA
Inheritance	One allele per locus from each parent
Steps	Extract DNA, amplify loci by PCR with labelled primers, separate by electrophoresis, compare patterns
Exclusion	A single clear mismatch shows two samples came from different individuals
Match	Matching at many loci makes a chance match very unlikely, but it does not prove guilt alone
Relationships	Every band in the child must be in the mother or the father
Plants and animals	Parentage in breeding programmes, avoiding inbreeding, identifying varieties, tracing illegally traded material

Method for a paternity or parentage question:

1. For each locus, remove the alleles that match the known parent.
2. The remaining allele must come from the other parent. If the child is homozygous, both parents carry it.
3. A candidate lacking any required allele is excluded.

Identical twins have the same profile, so profiling cannot separate them.

6.20 Time of death

Indicator	What changes	Main cautions
Decomposition	Autolysis then putrefaction by gut bacteria: colour change, gas, softening	Faster when warm, slower when cold or dry
Succession	Blowflies first, beetles and others later as the body dries	Access to the body and season affect arrivals
Forensic entomology	Age of larvae or pupae from length and stage, using development tables for the species and temperature	Gives a minimum time; warmth shortens development
Body temperature	Cools towards the surroundings	Air temperature, body size, clothing and wind change the rate
Muscle contraction	Rigor mortis: myosin stays bound to actin without ATP	Starts in small muscles; speed depends on temperature and activity before death

Rigor is not a clock. It starts in small muscles, spreads to larger ones, then passes as muscle proteins break down. Which stage the muscles have reached narrows the estimate, but it must be used with other evidence because warmth speeds the sequence and cold slows it.

Worked reminder: a body is 33.0 °C at 10:00. It was 37.0 °C at death and cooled 1.0 °C per hour (data given).

• Fall = 4.0 °C, so 4.0 hours.
• Death at about 06:00.

Explaining answers well

• For PCR, say what each component does and what temperature stage it works in. A list of ingredients alone rarely answers an explain question.
• For electrophoresis, link charge to direction and length to distance travelled.
• For DNA profiling, name the locus type (STR in non-coding DNA) and say that each person has two repeat numbers per locus.
• For time of death, name the indicator, say what has changed, and give the factor that limits its accuracy.
• For contamination, say that PCR amplifies any DNA present, so foreign DNA gives a false profile.

Must-know distinctions

• Primer annealing (about 50 to 65 °C) differs from extension (about 72 °C).
• PCR copies DNA; electrophoresis separates fragments. They are often used together.
• Saprotroph (microorganism) differs from detritivore (animal).
• Entomology gives a minimum time; body temperature gives an estimate that depends on surroundings.
• Exclusion needs one mismatch; inclusion needs matches at many loci.

Quick self-test

1. Why do saprotrophs secrete enzymes onto dead material?
2. Name the process by which saprotrophs return carbon to the atmosphere.
3. A bag holds 20.0 g of litter, which falls to 16.0 g over 40 days. Calculate the percentage loss and mean rate.
4. Why is Taq polymerase used rather than a human DNA polymerase?
5. State the purpose of the annealing stage.
6. 5 target molecules go through 20 cycles. How many copies are expected?
7. Why does DNA move towards the positive electrode?
8. Which moves further in a gel, a 300 bp or a 900 bp fragment, and why?
9. A child has repeat numbers 7 and 10 at a locus. The mother has 7 and 9. Which allele came from the father?
10. A body at 31.0 °C was found at 18:00. It was 37.0 °C at death and cooled at 1.5 °C per hour (data given). When did death occur, approximately?

Answers

1. Their digestion is extracellular, so large molecules are hydrolysed outside the cell and the small products absorbed.
2. Respiration, which releases carbon dioxide.
3. Loss = 4.0 g, so 4.0 / 20.0 × 100 = 20.0%; rate = 4.0 / 40 = 0.10 g per day.
4. Taq polymerase is heat-stable, so it is not denatured at about 95 °C and keeps working through repeated cycles.
5. Primers form hydrogen bonds with their complementary sequences at the ends of the target.
6. 5 × 2²⁰ = 5 × 1 048 576 = 5 242 880.
7. DNA is negatively charged because of its phosphate groups.
8. The 300 bp fragment, because it passes through the gel mesh more easily.
9. Allele 10, since the child’s other allele, 7, matches the mother (the father could also carry 7, but 10 must come from him).
10. Fall = 6.0 °C, so 6.0 / 1.5 = 4.0 h; death at about 14:00.

Where marks are usually lost

• Saying decomposers “eat” the body, without extracellular enzymes and absorption.
• Forgetting that respiration is the step that returns carbon dioxide.
• Writing “Taq works at high temperature” without saying it is not denatured.
• Mixing up annealing and extension temperatures or functions.
• Multiplying the starting number by 2 and the cycle number instead of raising 2 to the power of the cycle number.
• Saying DNA fragments move towards the negative electrode, or that longer fragments move further.
• Reading a size from a ladder by straight-line interpolation when the scale is logarithmic.
• Claiming a profile match proves identity, or giving one indicator as an exact time of death.

Official syllabus

Pearson Edexcel International Advanced Subsidiary/Advanced Level in Biology (YBI11), Specification Issue 2, February 2021, Pearson Education Limited: Topic 6, statements 6.16 to 6.20.