13.3.4

PCR & Gel Electrophoresis

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Polymerase Chain Reaction (PCR)

The polymerase chain reaction is used to amplify small amounts of DNA.

Polymerase chain reaction (PCR)

Polymerase chain reaction (PCR)

  • The polymerase chain reaction process enables us to take a small sample of DNA and produce many more copies of it, allowing for further analysis to take place.
PCR 'ingredients'

PCR 'ingredients'

  • Several ‘ingredients’ are required for the PCR reaction:
    • DNA primers (sections of DNA about 20 base pairs long which are complementary to the ends of the target sequence of DNA that you wish to amplify).
    • Free nucleotides adenine, thymine, guanine, and cytosine.
    • Taq polymerase (a special polymerase enzyme extracted from bacteria that live in very hot environments such as hot springs, so that the enzyme will not denature at the temperatures used in the PCR).
    • The target sequence of DNA that is to be amplified.
Thermal cycling

Thermal cycling

  • PCR is carried out in a thermocycler and involves a cycle of three steps at three different temperatures:
    • Denaturation at 95°C - DNA strands are separated by breaking the hydrogen bonds.
    • Annealing at 60°C - primers attach to complementary DNA by forming hydrogen bonds.
    • Elongation at 72°C - optimum temperature for Taq polymerase to add the free nucleotides to the exposed DNA strands.
  • These three steps are then repeated 20-30 times in a typical PCR reaction to potentially produce over 1,000,000,000 copies of the target sequence of DNA.

Gel Electrophoresis

Gel electrophoresis is used to separate proteins or fragments of DNA according to size. DNA profiling is a common application of gel electrophoresis.

Gel electrophoresis

Gel electrophoresis

  • Gel electrophoresis involves adding samples of proteins or DNA fragments to a gel immersed in a chamber with an electric current running through it.
  • The current causes the charged particles to move through the gel as it is porous.
  • The smaller particles can move through the gel more easily and therefore move further.
Analysis

Analysis

  • A banding pattern is formed which when compared to a reference can allow for the identification of specific proteins or DNA fragments.
DNA profiling

DNA profiling

  • DNA profiling, also known as DNA fingerprinting, is used to compare samples of DNA.
  • DNA profiling is commonly applied in forensic investigations and paternity testing.
  • The process involves both PCR and gel electrophoresis.
DNA profiling process

DNA profiling process

  • Firstly, PCR is used to amplify what could be a very small sample of DNA.
  • The amplified samples are then subjected to gel electrophoresis to compare them.
  • The bars of DNA fragments that form in the gel are compared to another reference e.g. with other suspects or evidence.
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1

Unity & Diversity - Molecules

1.1

Water

1.1.1Water & Hydrogen Bonding1.1.2IB Multiple Choice - Water & Hydrogen Bonding1.1.3Extended Response - Water
1.2

DNA Structure & Replication

1.2.1DNA1.2.2RNA1.2.3DNA Replication1.2.4DNA Replication - Summary1.2.5IB Multiple Choice - DNA Replication
1.3

Transcription & Gene Expression

1.3.1Introduction to Transcription & Protein Synthesis1.3.2Types of RNA1.3.3Transcription1.3.4RNA Processing in Eukaryotes1.3.5IB Multiple Choice - Transcription
1.4

Translation

1.4.1Translation1.4.2Retroviruses1.4.3Scientific Practices: Coronavirus1.4.4IB Multiple Choice - Translation
2

Unity & Diversity - Cells

2.1

The Origin of Cells

2.1.1Origins - Endosymbiosis
2.2

Introduction to Cells

2.2.1Introduction to Cells2.2.2Cell Size & Surface Area2.2.3Surface Area to Volume Ratio2.2.4Eukaryotic vs Prokaryotic Cells2.2.5Stem Cells2.2.6Stem Cells in Disease
2.3

Ultrastructure of Cells

2.3.1Golgi, Lysosomes & Ribosomes2.3.2Cell Walls & Vacuole2.3.3Prokaryotes2.3.4Binary Fission
2.4

Cell Division

2.4.1The Cell Cycle2.4.2Mitosis2.4.3Regulation of the Cell Cycle2.4.4End of Topic Quiz - The Cell Cycle2.4.5IB Multiple Choice - The Cell Cycle2.4.6Extended Response - Mitosis
2.5

Structure of DNA & RNA

2.5.1DNA & RNA
2.6

DNA Replication, Transcription & Translation

2.6.1Protein Synthesis2.6.2Transcription & Translation2.6.3End of Topic Test - DNA, Genes & Protein Synthesis2.6.4Exam-Style Question - Protein Synthesis2.6.5End of Topic Test - Coronavirus Translation2.6.6IB Multiple Choice - Transcription2.6.7IB Multiple Choice - Translation
2.7

Cell Respiration

2.7.1Overview of Respiration2.7.2Anaerobic Respiration2.7.3End of Topic Test - Anaerobic Respiration2.7.4Respiration Experiments2.7.5End of Topic Test - Respiration2.7.6IB Multiple Choice - Respiration
2.8

Photosynthesis

2.8.1Overview of Photosynthesis
2.9

Viruses

2.9.1Viruses
3

Unity & Diversity - Organisms

3.1

Diversity of Organisms

3.1.1Chromosomal Theory of Inheritance3.1.2Chromosomal Basis of Inherited Disorders3.1.3IB Multiple Choice - Chromosomal Inheritance
3.2

Evidence for Evolution

3.2.1Evidence for Evolution - Fossils & DNA3.2.2Evidence for Evolution - Anatomy & Geography3.2.3IB Multiple Choice - Evidence for Evolution3.2.4Extended Response - DNA & Evolution
3.3

Natural Selection

3.3.1Introduction3.3.2Evolutionary Fitness3.3.3Natural Selection & Variation3.3.4End of Topic Quiz - Natural Selection3.3.5IB Multiple Choice - Natural Selection3.3.6Speciation
4

Unity & Diversity - Ecosystems

4.1

Classification

4.1.1Introduction to Biodiversity4.1.2Keystone Species4.1.3Courtship & Ancestry4.1.4Classification
4.2

Cladistics

4.2.1Evolutionary Relationships4.2.2IB Multiple Choice - Species & Taxonomy
4.3

Evolution & Speciation

4.3.1Evidence for Evolution - Fossils & DNA4.3.2Evidence for Evolution - Anatomy & Geography4.3.3IB Multiple Choice - Evidence for Evolution4.3.4Extended Response - DNA & Evolution4.3.5Populations4.3.6Mutations, Genetic Drift, & Gene Flow4.3.7Speciation4.3.8Rate of Speciation4.3.9Allopatric & Sympatric Speciation
4.4

Conservation of Biodiversity

4.4.1Coming Soon!
5

Form & Function - Molecules

5.1

Carbohydrates & Lipids

5.1.1Monosaccharides5.1.2Disaccharides & Polysaccharides5.1.3Triglycerides & Phospholipids5.1.4Cellulose5.1.5Starch & Glycogen
5.2

Proteins

5.2.1Structure & Functions of Proteins
6

Form & Function - Cells

6.1

Membranes & Membrane Transport

6.1.1Passive Movement Across Membranes6.1.2Active Movement Across Membranes6.1.3Endocytosis & Exocystosis6.1.4Cell Membrane Structure & Permeability
6.2

Organelles & Compartmentalization

6.2.1Eukaryotic Cells & Organelles6.2.2Subcellular Components & Organelles
6.3

Cell Specialization

6.3.1Cell Specialization
7

Form & Function - Organisms

7.1

Gas Exchange

7.1.1Lung Structure & Alveoli7.1.2Ventilation7.1.3Lung Disease7.1.4Lung Disease Data
7.2

Transport

7.2.1The Circulatory System7.2.2The Heart7.2.3Blood Vessels7.2.4Cardiovascular Disease7.2.5Xylem Structure7.2.6Cohesion-Tension Theory7.2.7Investigating Transpiration Rate7.2.8Phloem Structure7.2.9Translocation
7.3

Muscle & Motility

7.3.1Skeletal Muscle7.3.2Sliding Filament Theory7.3.3Contraction
8

Form & Function - Ecosystems

8.1

Species, Communities & Ecosytems

8.1.1Population Dynamics8.1.2Communities & Measuring Diversity8.1.3Relationships Between Populations8.1.4Overview of Ecosystems8.1.5Nutrient Cycles8.1.6Fertilisers8.1.7Eutrophication8.1.8Chi-Squared Test
8.2

Energy Flow

8.2.1Energy8.2.2Energy Flow8.2.3Biomass & Food Chains8.2.4Heterotrophs & Autotrophs
8.3

Carbon Cycle

8.3.1Carbon Cycle
8.4

Climate Change

8.4.1Carbon Dioxide8.4.2The Greenhouse Effect8.4.3Global Warming8.4.4Maintaining Biodiversity
9

Interaction & Interdependence - Molecules

9.1

Enzymes

9.1.1Enzymes9.1.2Factors Affecting Enzyme Activity9.1.3Enzyme-Controlled Reactions9.1.4End of Topic Test - Enzymes
9.2

Metabolism

9.2.1Molecules to Metabolism
9.3

Cell Respiration

9.3.1Glycolysis9.3.2Aerobic Respiration
9.4

Photosynthesis

9.4.1Light-Dependent Reaction9.4.2Light-Independent Reaction9.4.3End of Topic Test - Photosynthesis Reactions9.4.4Limiting Factors9.4.5Photosynthesis Experiments9.4.6End of Topic Test - Photosynthesis9.4.7End of Topic Test - Photosynthesis
10

Interaction & Interdependence - Cells

10.1

Chemical Signalling

10.1.1Coming Soon!
10.2

Neural Signalling

10.2.1Medical Application10.2.2Speed of Transmission10.2.3Synapses10.2.4End of Topic Test - Nervous Comm&Coord10.2.5Neuron Structure10.2.6Types of Synapse10.2.7End of Topic Test - Neurones & Action Potentials10.2.8Transmission of an Impulse10.2.9End of Topic Test - Synapses
10.3

Adaptation to Environment

10.3.1Coming Soon!
10.4

Ecological Niches

10.4.1Coming Soon!
11

Interaction & Interdependence - Organisms

11.1

Integration of Body Systems

11.1.1Plant Tropisms
11.2

Defence Against Disease

11.2.1Immune System11.2.2The Immune Response11.2.3Antibodies11.2.4Primary & Secondary Response11.2.5Vaccines11.2.6HIV11.2.7End of Topic Test - Immune System
12

Interaction & Interdependence - Ecosystems

12.1

Populations & Communities

12.1.1Coming Soon!
12.2

Transfers of Energy & Matter

12.2.1Coming Soon!
13

Continuity & Change - Molecules

13.1

DNA Replication

13.1.1DNA Replication
13.2

Protein Synthesis

13.2.1Protein Synthesis13.2.2Transcription & Translation13.2.3End of Topic Test - DNA, Genes & Protein Synthesis
13.3

Mutation & Gene Editing

13.3.1Genes13.3.2Mutations13.3.3DNA Technology13.3.4PCR & Gel Electrophoresis13.3.5Genetic Modification13.3.6Cloning
14

Continuity & Change - Cells

14.1

Gene Expression

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14.2

Water Potential

14.2.1Controlling Blood Water Potential
15

Continuity & Change - Organisms

15.1

Inheritance

15.1.1Non-Nuclear Inheritance15.1.2Linked Genes15.1.3IB Multiple Choice - Non-Mendelian Genetics15.1.4Extended Response - Inheritance15.1.5Introduction to Non-Mendelian Inheritance15.1.6Chi-Squared Test15.1.7End of Topic Quiz - Inheritance15.1.8Sex-Linked Genes15.1.9Grade 4-5 (Scientific Practices) - Inheritance
15.2

Homeostasis

15.2.1Overview of Homeostasis15.2.2Blood Glucose Concentration15.2.3Controlling Blood Glucose Concentration15.2.4End of Topic Test - Blood Glucose15.2.5Type I & Type II Diabetes15.2.6Human Reproductive Systems15.2.7Hormonal Control of the Menstrual Cycle15.2.8Kidneys & Osmoregulation
16

Continuity & Change - Ecosystems

16.1

Natural Selection

16.1.1Natural Selection
16.2

Stability & Change

16.2.1Coming Soon!
16.3

Climate Change

16.3.1Carbon Dioxide16.3.2The Greenhouse Effect16.3.3Global Warming16.3.4Maintaining Biodiversity

Practice questions on PCR & Gel Electrophoresis

Can you answer these? Test yourself with free interactive practice on Seneca — used by over 10 million students.

  1. 1
    Which of these is NOT an ingredient required for the PCR reaction?Multiple choice
  2. 2
    Which of these is NOT a key step in the PCR reaction?Multiple choice
  3. 3
    Which of the following DNA fragments will move furthest through the gel in gel electrophoresis? The fragment length in number of base pairs (bp) is given.Multiple choice
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