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D1.1Theme D — Continuity and change

DNA replication — IB Biology SL Revision Notes & Topical Questions

5 min read 12 parts Lesson 2 of 14 2 quizzes

📚 IB Biology SL Hub / Topical Revision
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Curriculum Equation Key قوانين الرقم الهيدروجيني والاتزان الأيوني - pH & Acid-Base Equilibrium FormulasFast Exam Solution
pH = -log[H⁺] | pOH = -log[OH⁻] | pH + pOH = 14 | [H⁺][OH⁻] = 10⁻¹⁴
Word Equation & Conditions: الرقم الهيدروجيني = -لوغاريتم تركيز أيون الهيدروجين | pH + pOH = 14
Location & Specifications: الاتزان الأيوني، كيمياء 3 ثانوي، التحصيلي، و AP Chemistry.
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Lesson summary

D1.1 DNA replication — IB BIOLOGY SL notes: Explain semi-conservative DNA replication and the uses of PCR, gel electrophoresis and DNA profiling.Purpose — each daughter cell needs a full copy of the genomeGrowth: new cells in a developing body each need identical DNA.Repair: worn…

  • Parent cell compared with parent organism
  • Semi-conservative replication
  • DNA polymerase
  • Hypothesis
  • Conclusion
  • Thermal cycler

Part 1 of 10Why DNA is replicated

Why DNA is replicated
Purpose
  • Purpose each daughter cell needs a full copy of the genome
  • Growthnew cells in a developing body each need identical DNA.
  • Repairworn or damaged cells such as skin and gut lining are replaced.
  • Reproductioncopies are needed before cell division in single-celled organisms and before gamete formation.
Timing
  • Timing replication occurs in S phase of interphase, in the nucleus in eukaryotes, before mitosis
Parent cell compared with parent organism
  • Parent cell compared with parent organism a parent cell is any cell that divides, whereas a parent organism is the individual

Part 2 of 10Semi-conservative replication

Semi-conservative DNA replication
Semi-conservative DNA replication
1Semi-conservative replication
Semi-conservative replication each new DNA molecule keeps one original strand and has one newly built strand
  • The kept strand is the template strand.
  • Free nucleotides from the nucleus are added one by one by complementary base pairing.
  • Adenine pairs with thymine and cytosine pairs with guanine.
  • Hydrogen bonds form only if the bases are correctly paired.
2Accuracy
  • Accuracy the original strand guides the new one, so copies are almost identical
  • It keeps genetic continuity between generations of cells.
  • Rare errors are mutations, and an uncorrected mispaired base is copied into later generations.

Part 3 of 10Helicase and DNA polymerase

1
Helicase unwinds the double helix, using energy from ATP, and breaks the hydrogen bonds between bases.
2
Each strand is exposed as a template at the replication fork.
3
Free nucleotides pair with the exposed template bases.
4
DNA polymerase joins the nucleotides by condensation reactions into a new strand.
5
Two identical DNA molecules result.
  • DNA polymerase
    • forms covalent bonds between the deoxyribose and phosphate of adjacent nucleotides, making the sugar-phosphate backbone
    • It always builds the new strand in the 5′ to 3′ direction.
    • It reads the template strand in the 3′ to 5′ direction.
    • The strands are antiparallel, so the new strands are built in opposite directions.

Part 4 of 10Evidence for semi-conservative replication

Hypothesis
  • Watson and Crick proposed semi-conservative replication when they described the double helix
Test by Meselson and Stahl
1
Bacteria were grown in heavy 15N and then moved to light 14N.
2
DNA was spun in a density gradient so it formed bands by density.
3
After one generation there was one intermediate band.
4
After two generations there were intermediate and light bands.
  • Conclusion
    • the results rule out conservative replication and support the semi-conservative model

Part 5 of 10Gel electrophoresis

  • Gel electrophoresis = separation of molecules by size and charge using an electric current
    • DNA is negatively charged because of its phosphate groups, so it moves towards the anode, the positive pole.
    • Smaller fragments move faster and further through the pores of the gel.
    • The type of gel affects the speed, with agarose for DNA and polyacrylamide for proteins.
1
Make an agarose gel in a tank with wells cut at the cathode end.
2
Submerge the gel in an electrolyte solution.
3
Load the DNA fragments into the wells with a micropipette.
4
Switch on the current so the DNA fragments move towards the anode.
5
Run a ladder of known sizes alongside to estimate fragment sizes.
6
Transfer the fragments to absorbent paper or nitrocellulose and add probes.
7
Show the bands with a radioactive label on X-ray film, or a fluorescent dye under UV light.

Part 6 of 10Polymerase chain reaction

1PCR
PCR an in vitro method of amplifying a specific DNA sequence from a very small sample, even one molecule
  • It gives billions of copies in a few hours.
2
Requirements
  • Target DNA, which may be a single molecule from hair or blood.
  • Two primers, one for each strand end, that mark the target boundaries.
  • Taq polymerase from the thermophilic bacterium Thermus aquaticus, which does not denature at high temperature.
  • Free nucleotides.
  • A buffer for the optimum pH.
3Thermal cycler
  • Thermal cycler a machine that automatically sets the temperature and timing of each stage

Part 7 of 10One PCR cycle

1
Denaturation: heat to about 95 °C so the hydrogen bonds break and the strands separate.
2
Annealing: cool to about 50-60 °C so the primers bind to the ends of the single strands.
3
Extension: warm to 72 °C for at least a minute so Taq polymerase builds the complementary strands.
4
The amount of target DNA doubles.
1Amplification
  • 20 cycles give about a million molecules and 30 cycles give about a billion copies
2
Comparison with cell replication
FeatureCell replicationPCR
Strand separationHelicaseHeating to about 95 °C
PolymeraseThe cell's own DNA polymeraseTaq polymerase
Region copiedWhole genomeShort target sequence
LocationNucleus in S phaseThermal cycler

Part 8 of 10DNA profiling

  • DNA profiling = comparing the patterns of VNTRs to identify people or relationships
    • VNTRs are variable number tandem repeats, short non-coding regions 20-50 bases long.
    • Everyone except identical twins has a unique combination.
1
Extract DNA from, for example, a hair root, blood, semen or saliva.
2
Amplify it by PCR.
3
Cut the DNA into fragments with restriction endonucleases.
4
Separate the fragments by size with gel electrophoresis.
5
Add radioactive or fluorescent probes that are complementary to the VNTRs.
6
Visualise the probes with X-ray film or UV light.
7
Analyse and compare the pattern of bands.
  • Viral testing
    • PCR detects viral sequences, as in COVID-19, and viral RNA is first copied into DNA and then amplified

Part 9 of 10Interpreting profiles

Paternity
  • Paternity every band in the child must come from the mother or the father
  • A band the mother lacks must come from the father, so men lacking it are excluded.
  • A parent shares about 50% of the child's bands.
Forensic match
  • Forensic match the suspect's bands must align with all the bands from the crime scene
  • One clear mismatch rules a person out.
  • Samples are compared with the victim, suspects and control samples, and contamination must be avoided.
Ancestry
  • Ancestry profiles can identify parents or other ancestors
Reliability
  • Reliability comparing more VNTRs lowers the chance of a false match
Ethics
  • Ethics storing profiles raises privacy questions

Part 10 of 10More from the specification

1Semi-conservative replication
  • DNA helicase unwinds the double helix, and DNA polymerase synthesizes a complementary strand alongside each pre-existing template strand.
2DNA polymerase directionality
  • DNA polymerase links nucleotides exclusively in the 5' to 3' direction, forming covalent phosphodiester bonds.
3Polymerase chain reaction (PCR)
  • A cyclic laboratory technique using heat-stable Taq polymerase and oligonucleotide primers to create millions of target DNA copies.
4Gel electrophoresis profiling
  • Separation of fragmented DNA by electric charge and size to determine whether individuals possess matching parental allele bands.

Key terms

TermMeaning
Semi-conservative replicationReplication in which each new DNA molecule contains one original strand and one new strand.
HelicaseThe enzyme that unwinds the DNA and breaks the hydrogen bonds between bases.
DNA polymeraseThe enzyme that joins nucleotides to build a new DNA strand on a template.
PCRThe polymerase chain reaction, which amplifies a target DNA sequence in vitro.
Gel electrophoresisA technique that separates charged molecules by size in a gel using an electric current.
PrimerA short DNA sequence that binds to the end of a target and starts DNA synthesis.
VNTRA variable number tandem repeat, a short repeating non-coding DNA sequence used in DNA profiling.
Taq polymeraseA heat-stable DNA polymerase from Thermus aquaticus used in PCR.

Avoid these mistakes

1
Saying DNA replication makes one old and one new molecule — each new molecule has one old and one new strand
2
Saying DNA polymerase unwinds the DNA — helicase unwinds it and polymerase builds the new strand
3
Saying DNA moves to the negative pole — it is negatively charged and moves to the positive pole
4
Saying Taq polymerase is used because it is fast — it survives the high temperature of denaturation

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  • RNA: 5′ → 3′ 3′ → 5′.
  • : AUG UAC .
  • : UAA, UAG, UGA tRNA (Release Factor) .
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