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Drugs, Detectives and DNA

B02: Unit 2: DNA Analysis


Unit 2: DNA Analysis

Lesson Plans Unit 2 (90 minute classes)

Lesson Plan 1

  1. Student Notes on DNA extraction from Strawberries or Saliva
  2. DNA extraction from Strawberries or Saliva
  3. Introduction to Biotechnology equipment and supplies, practice pipetting with colored water and changing the settings.

Lesson Plan 2

  1. Practice micropipetting with 10% glycerol and different food dyes.
  2. Make 1X TBE from a stock solution. Review making solutions M1V1 = M2V2
  3. Pour 0.8% agarose in 1X TBE to be used in next class.
  4. DNA goes to the Race – paper simulation of restriction enzyme analysis (Kreuzer and Massey)

Lesson Plan 3

  1. Electrophoresis of dyes (Carolina Biological Company Kit#: 21-1002)
  2. Student Notes on Electrophoresis and Restriction Enzymes and DNA Fingerprinting from Boston University’s CityLab “Case of the Missing Crown Jewels” (
  3. Prelab activity for the Boston University’s CityLab “Case of the Missing Crown Jewels”

Lesson Plan 4

  1. Analyze dye electrophoresis gels.
  2. Pour more gels for Restriction analysis of Lambda DNA (Carolina Biological Company Kit # MR-21-1149)
  3. Digest DNA with restriction enzymes to run on an electrophoresis gel in next class.

Lesson Plan 5

  1. Run gels of digested DNA (Restriction analysis of Lambda -Carolina Biological Company Kit # MR-21-1149) for 30-60 minutes.
  2. Show Video “Footpath Murders” while gel runs.
  3. Analyze gels run with DNA cut with restriction enzymes.

Lesson Plan 6

  1. Notes on PCR (polymerase chain reaction)
  2. PCR PowerPoint from Dr. Stefan Franzen’s Polymerase Chain Reaction (PCR ppt)

Lesson Plan 7

  1. DNA fingerprinting activity: “The Case of the Missing Crown Jewels”
  2. Analysis of DNA fingerprinting in order to determine the guilty person.

Resources and References:


  1. Kreuzer, Helen and Massey, Adrianne. “Recombinant DNA and Biotechnology: A Guide for Teachers.” American Society for Microbiology Press. 1325 Massachusetts Avenue, N.W. Washington D.C. 20005. Copyright 1996. ISBN: 1-55581-101-9
  2. Micklos, David A. and Freyer, Greg, A., “DNA Science”: A First Course in Recombinant DNA Technology. Cold Spring Harbor Press and Carolina Biological Supply Company. 1990. ISBN 0-89278-411-3

Unit 2 Video:

  1. "Footpath Murders" Medical Detectives: Explorations in Forensic Science, available at ISBN Number: 0-7365-0449-4

Websites of Interest:

  1. These outreach programs include the ones from Boston University used in the City Lab Modules I have used in conjunction with UNC-Chapel Hill Department of Biology i.e. NIH Curriculum Supplement Series including Human Genetic Variation, Cell Biology and Cancer. In addition, the site also has more great links for educators.
  3. (Modules used by UNC destiny bus includes “Case of the Missing Jewels” – A DNA Fingerprinting module and “The Crooked Cell” – Sickle Cell Module.

Unit 2: DNA Analysis

  • Lab 1: DNA Extraction with strawberries or with saliva.
    • Activity 1: Inventory of equipment and supplies and practice micropipetting with water colored with food dye.
    • Activity 2: Practice micropipetting into 1% agar gel in Petri plates using combs from electrophoresis chambers to make multiple wells.
    • Activity 3: Make 1x TBE buffer and Pour .8% agarose electrophoresis gels
    • Activity 4: DNA goes to the Races – paper simulation of restriction enzyme analysis (Kreuzer and Massey) p.171
  • Lab 2: Electrophoresis of Dyes (Carolina Biological Supply kit #21-1002)
  • Lab 3: Restriction Analysis of Lambda DNA (Carolina Biological Supply kit #MR-21-1149)
  • Lab 4: "Case of the Missing Crown Jewels": DNA fingerprinting Activity from Boston University City Lab and UNC Chapel Hill Destiny Bus PMABS.
Supplemental Information: 

Biotechnology Student Notes

Unit II: Genes, Genetics and Geneticists:

Genes: What are they? What do they do? How do they do it? How are we using them?
Key terms: Central Dogma, DNA, RNA, proteins, Carbohydrates, AA, and Nucleotides

Historical Milestones:

  1. Mendel - Discrete nature of genes
  2. Chemical nature of genes: Transforming Factor = DNA, DNA from dead mice and injected bacteria containing pneumonia strain
  3. Hershey and Chase experiment used radioactive isotope which was injected into phage. The DNA went in but left the protein coat behind indicating that DNA was the genetic material passed on to the next generation
  4. Structure of DNA:
    1. Physicist, Maurice Wilkins and Rosalind Franklin: X-ray diffraction work showed the presence of a double helix in DNA
    2. Chargaff: A=T and G=C
    3. Linus Pauling: alpha helix
    4. Watson and Crick: determined the DNA structure of a double helix with complementary base pairing of nucleotides
  5. Central Dogma: DNA -> RNA -> Protein
  6. Dogma Revision: Exon is meaningful, Intron excised and not used, transposons jump and RNA can act as an enzyme


  1. Code for Proteins
  2. Located on Chromosomes
  3. Replicate themselves
  4. Act as a blueprint
  5. Determine who we are


  1. Genetic variation
  2. Mutations: misread, deletions, insertions
  3. Effects of mutations
  4. Natural Selection

Molecular Biology:

  1. DNA Structure: ATGC, phosphodiester bonds. Hydrogen bonds, complementary base pairs form the double helix.
  2. DNA function: faithful replication.
  3. DNA function: information transmission, proteins, genetic code, triplets are codons, one gene, one protein and an entire set of genes is a genome.
  4. Protein Synthesis: tRNA carries AA, mRNA codes for protein, TRANSCRIPTION is from DNA to mRNA.
  5. mRNA -> Protein is TRANSLATION, initiation codon, AUG, and stop codons, UAG,UGA and UAA
  6. Eukaryotes vs Prokaryotes
  7. Gene Regulation; repressors, operons e.g. lactose operon, transcriptional activators or transcription factors, enhancers p. 65

Genomic Organization:

  1. Chromosomes, chromatin, plasmids, virus genomes and viruses are used as tools in Biotechnology
  2. Noncoding DNA is junk DNA
  3. Mutations; most are fixed with DNA repair enzymes

Protein Structure and Function:

  1. Amino Acids and Peptide Bonds
  2. Polar and Nonpolar covalent bonds

    1. Polarity and stability: hydrophobic and hydrophilic
    2. Hydrogen bonds
  3. Fundamental structure:

    1. Primary sequence of amino acids in a polypeptide.
    2. Secondary: Hydrophilic backbone folds so that hydrophobic amino acids are in the interior creating a water free hydrophobic environment: two arrangements which use hydrogen bonding are the alpha helix and the beta sheet.
    3. Tertiary Structure: How the fundamental DOMAINS fit together using hydrogen bonds, hydrophobic interactions, disulfide bridges, covalent and ionic bonds. These atomic interactions give the molecules their shape and eventually their function.
    4. Quaternary Structure: more than one polypeptide chain fit together, ex. Hemoglobin has 2 alpha subunits and 2 beta subunits. Not all molecules have a quaternary structure.

References and Resources:
Lehninger, "Biochemistry"
Sheenan, M. "Biochemistry and Molecular Biology", University of Bath 16-19 Series, Nelson, 1994 ISBN 0 17 4482078
Barnum, Susan R. "Biotechnology"Kruezer, Helen, "Recombinant DNA and Biotechnology" Laboratory Resource Materials City Lab Curriculum from Boston University in conjunction with UNC-Chapel Hill Department of Biology
NIH Curriculum Supplement Series including Human Genetic Variation, Cell Biology and Cancer, The Brain: Understanding Neurobiology through the Study of Addiction

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