Module 2 Links

Module 2 – Genes and Genetic Engineering

Links to Teaching Resources

Jump to: DNA, Chromosomes, Mitosis, Asexual reproduction, Sexual reproduction,= Genetic engineering techniques= , Genetic engineering applications= , Gene Therapy, = Human genome project

      Countdown= Timer from Echalk. Very useful!

DNA<= o:p>

DNA Structure=

      DNA PowerPoint Useful picture= s, but needs sorting.

      Nucleotide structure from Starr, showing 4 bases. Good.

      DNA structure in detail from Starr. Good.

      DNA structure from Sumanas, using Rasmol. Slow and detailed, but good.

      Base pairing game from DNAi (go to Code-Finding the structure-P= utting it together-Base pairing game). Very difficult exercise in matching up puri= ne and pyrimidine nucleotides. Worth doing to show how difficult it is!

      The original Watson-Crick papers 1, 2, 3, 4, 5 (local) and online from Nature= archives

      DNA overview from Starr. Not working.

      DNA structure from Alberts ECB (local). Detailed Chime presentation, probab= ly too detailed.

      Nucleic acid pairs game from Brooks/Cole

      Label a DNA molecule from John Wiley

      3D DNA molecule from 3dscience

      DNA history= , One gene-one pr= otein, Genes are ma= de of DNA, DNA structure from DNA from the beginning. Interesting background stories a= nd research. Good for further reading.

DNA Structure= – Background/less useful

      Introduction to DNA from DNAi (go to Code-Finding the structure-Problem-Introduction to DNA). About the history of DNA. OK.

      DNA structure from John Kyrk. Detailed, but not friendly.

      DNA structure from Kardong. Quite good.

      DNA Struct= ure using Rasmol from ? Simple, not as good as Kardong.

      DNA from AS Guru. Quite good.

      DNA from blobs.org

      DNA from Western Kentucky

      Nucleotides<= /a> from blobs.org

      The secret of Photo 51 from Nova. Lots of interesting background about the discovery of the structure of DNA. Photo 51 is Rosalind Franklin’s fa= mous x-ray diffraction photo of DNA.

      G= riffith experiment from Starr showing DNA as the hereditary material. Nice, but= not needed.

      Hershey-Chase experiment from Starr

      Hershey-Chase from Mader

      Introduction to genetics<= /a> from GlaxoSmithKline. Not as good as other sites.

      DNA workshop from PBS. A bit dull.

      Molecular = Genetics from Miami. Quite good background information.

      DNA cartoons on PowerPoint.

      Gene Almanac= from Dolan DNA learning Centre. Downloadable animations from the DNAi websi= te. Exe files, so can’t run on network. Use DNAi site instead.

      DNA50 from the NCBE. Lots of interesting trivia to mark the 50^th anniversary of the discovery of the structure of DNA

      Exploring DNA from the Laboratory of Molecular Biology at = Cambridge. Good tutorial, but you need = to download and install the “Chime” add-in to see the diagrams. Instructions are on the site.

      Left Handed = DNA. The DNA molecule is a right-handed helix (like a screw). But many textbooks= and web sites get it wrong and give a left-handed helix. This site names and sh= ames hundreds of these mistakes!

      Oxford Ancestors. A = novel application of DNA technology. “Oxford Ancestors” is run by scientists from Oxford University, and for £150 they will analyse your DNA and tell you where your ancestors came from ten thousand years ago.

Replication

      DNA replication from Starr, showing semi-conservative replication. Very nic= e, with quiz at end.

      DNA rep= lication (local) from Benjamin Cummings. Very nice 3Dish animation, without narratio= n, but worth showing. Shows Okasaki fragments, but in a simple way. Also more advanced version (local) with narration, showing replication fork and primer RNA. Also good.

      DNA replication (local from Alberts ECB) or online from DNAi (go to Code-Cop= ying the code-Putting it together-Replication). Amazing animation showing the molecular machinery of DNA replication. Also more detailed, English version= on DNA interactive DVD.

      DNA replication from Mader. Detailed but nice, introducing problem of laggi= ng strand. Also more detailed animation for more details of Oksaki fragment.

      DNA polymerase and clamp prote= in from Alberts ECB (both local)

Messelson-Sta= hl Experiment

      Messelson-Stahl experiment from Mader. Brilliant!

      Messelson-Stahl experiment from DNAi (go to Code-Copying the code-Pieces of the puzzle-= semiconservative replication). Step-by step animation. Very good.

      Messelson-Stahl experiment from Lifewire and from Suamanas.

      Messelson-Stahl experiment from DNA from the beginning.

      Mes= selson Stahl experiment from Lehninger. A good pdf document for further readin= g.

Replication – less useful

      DNA replication fr= om John Kyrk. Detailed but not very friendly.

      DNA replication from Lifewire. Also part 2 about leading and lagging strands.

      DNA replication from Alberts (local). Shows detailed of Okasaki fragments. Nice, but Way too complex.

      DNA replication (local). Very Detailed, showing Okasaki fragments.

      DNA replic= ation (local) from Benjamin Cummings. Not good.

      DNA replication from Boyer (choose DNA replication). Not as good as others.=

      DNA= replication animation (local). Not very good.

      DNA replication in bacteria from Mader. OK, but not really relevant.

      DNA replication from Lew_port’s Biology Place. Amateur.

      DNA Gyrase (local). Groovy, but not really relevant.

      Telomerase from Alberts. Not needed, but interesting.

Transcription

      Transcription from Starr. Spot on – use.

      Transcription from Benjamin Cummings (local). Very appropriate, though not all that prett= y.

      Transcription from Mader. Nice, but not as good as Starr.

      Transcription from Lifewire

      Transcription (local) or online from from DNAi (go to Code-Copying the code-Putting it together-Transcription). Amazing animation showing the molecular machinery of RNA transcription. Also more detailed, English version on DNA interactive DVD.

      RNA polymerase game from DNAi (go to Code-Copying the code-Putting it together-RNA pol game). Be RNA polymerase and make mRNA.

      mRNA from D= NA from the beginning.

mRNA Processi= ng

      mRNA processing from Starr, showing introns and exons. Simple description at about the right level. Good.

      mRNA processing from Mader. Nice little animation showing how introns are removed.

      mRNA processing from LifeWire.

      mRNA processing from Alberts ECB (local) and from online from Sumanas. Fairly simple animation of splicing.

      mRNA processing= from DNA from the beginning.

Transcription= – less useful

      DNA transcription from John Kyrk. Not friendly.

      Types of RNA= from blobs.org

      Tra= nscription from MCBE. Slow download. Very pretty, but way too advanced (e.g. TATA box). Don’t use.

      RNA processing from MCBE. Big movie, but way too complicated. Not needed.
      RNA = splicing from MCBE, showing introns, exons and splicesomes. Too complex.

      mRNA slicing from Lehninger. Nice, but too complicated.

      mRNA processing from Sumanas. Too complicated.

      Control of transcription from Lifewire

      Gene Regulation from Johnson Explorations

Translation

      Genetic code demo from Starr. Very simple, but could be fun.

      Tr= anslation from Kardong. Nice.

      Translation from Mader. Good.

      Trans= lation from MCBE. Big download, and too much detail, but rather nice.

      Translation (local from Alberts ECB) or online from from DNAi (go to Code-Reading the code-Putting it together-Translation). Amazing animation showing the molecular machinery of protein synthesis. Also more detailed, English version on DNA interactive DVD.

      Transl= ation from Brooks/Cole

      Ribosome game from DNAi (go to Code-Reading the code-Putting it together-Ribosome game). Be a ribosome and match amino acids to codons to make protein.

      = Polyribosomes (local from Alberts ECB) and Online from Sumanas. Nice.

      tRNA= from Alberts ECB. Chime presentation showing tRNA structure in detail.

      Genetic code and gene expression= from DNA from the beginning.

Translation &= #8211; less useful

      Translation from Benjamin Cummings. Simple, and not as good as others.

      Translation from Lifewire

      Translation from J= ohn Kyrk. Not friendly.

      Translation from Alberts ECB (local). OK, but brief, and not as good as others.

      Translation in Eukaryotes from Alberts ECB (local)

      Translation from Starr. Disappointing, not as good as others.

      Translation from Boyer (choose protein synthesis). Quite nice, but too much detail, and probably not as good as others.

      Translation<= /a> from blobs.org

      Translation from lew-Port’s Biol= ogy Place. Poor.

      Life cycle of a protein from Sumanas, with details of protein folding, chape= rone proteins, and degredation. Not needed.

      Protein secretion from Sumanas. Not needed.

      Deciphering the genetic code from lifewire

Mutations

      Addition and Deletion mutations from Mader. Good.

      Addition and Deletion mutation (local). Showing details of how they happe= n by chain slippage. Good.

      Substitution mutation from Starr. OK, includes DNA repair.

      Mutations from Kardong. Not really correct.

      Insertion mutation from Starr showing effect of frame shift on resulting protein.=

      Chromosome mutations from Mader. Not needed, but quite interesting.

      DNA mutations = from Cancerquest. Good for background information.

      Mutations a= nd mutation repair= from DNA from the beginning.

Chro= mosomes

      Chromosome powerpoint

Chromosome co= iling

      DNA and chromosomes from Welcome. Zoom in from whole body to DNA.

      Chromosome coiling from Starr. From chromosome to DNA step-by-step. Nice.

      Chromosome Coiling (local from Alberts ECB) or online from online from DNAi (choo= se Genome-tour-chromosome close-up). Also more detailed, English version on DNA interactive DVD.

      DNA packing= from DNA from the beginning.

Karyotypes

      = Karyotype from Starr, showing how to do it.

      Interactive karyotype from University of Utah<= /st1:PlaceName>. Great fun automated and interactive human karyotypes.

      Karyotype Gizmo from ExploreLearning. Nice karyotype sorting activity, with quest= ions too.

      Abnorm= al Karyotypes from Miami= University. Also an animated karyotype.

      Karyotype activity from Arizona Biology project. Dull.

      New Karyotyping from Arizona Biology project

Gene Loci

      Gene loci from DNAi (Genome-Tour-Flyover-Chromosome = intro). Zooming into end of chromosome to look at globin gene cluster. Very nice.
      Gene browser from Welcome (choose chromosome browser). Very nice browser, where you can read about various genes on each chromosome.

      Gene browser from DNAi (Genome-Tour-Genome spots). C= lick on selected loci to learn about the genes there. Similar to Welcome.

      Gene browser from DNAi (Genome-Tour-FISHing). Links = to the NCBI genome map viewer. High-powered, but could be useful.

      GeneCards. Serious and complex, but could be good project.

Chromosomes &= #8211; less useful

      DNA coiling from Stryer (local from Freeman) or online from Biostudio and from Lehninger. Bit dull.

      Chromosome struct= ure from John Kyrk

Mito= sis

Cell Cycle

      Ce= ll cycle from Mader. Very good, also more complex version.

      Cell cycle from Freeman. OK.

      Cell cycle from Starr. Click on each stage. OK.

      Cell cycle and cancer from Mader. Not needed, but quite interesting.

      Cell cycle game from Mader. Interactive game identifying cancer cells. Nice.=

      Regulating the Cell cycle from Johnson Explorations

Mitosis Movie= s

      Plant mitosis movie from Alberts ECB (local). Good for chromosome shortening.

      Animal Mitosis Mo= vie from Alberts ECB (local)

      Mitosis movie of Newt cells (local)

      Mitotic cell from Alberts (local) showing fluorescent spindles.

      Mitosis in embryo= cells from Alberts (local), showing fluorescent spindles.

      Mit= osis photos from Molecular Expressions. Standard onion root tip cells.

      Mitosis world. Source of many movies, many rather technical.

Mitosis Anima= tions

      Stages of mitosis from Starr. Step-by step, with either photos or diagrams. Ni= ce.

      Mitosis from Raven and Johnson. Very good. Same but different colours from Mader

      Mitosis to music from the Wisconsin WORM initiative. Nice!

      3D= Mitosis from Starr. Long download, but very nice. **DOWNLOAD**

      3D Mitosis (local) from Hybrid animations. Awesome journey into nucleus. C= ool!

      Mit= osis animation (local) showing alleles.

      Label mitosis games from Mader. Three labelling activities – all good.<= /p>
      Interactive mitosis quiz from Starr. Drag-and-drop. Nice.

      Mit= osis from Molecular Expressions. Step-by-step. OK.

      Cytoplasm division in animals and plants from Starr

Mitosis ̵= 1; less useful

      Cell Cycle from Cells Alive. Not as good as others.

      Cell Cycle and Mitosis from Ar= izona Biology Project. Dull.

      Mitosis from John Kyrk

      Mitosis from Cells Alive. Not as good as others.

      Mitosis from AS Guru

Asex= ual Reproduction

Cloning Plant= s

      Powerpoint (local) of Plant micropropagation from Texas A&M University.

      = Plant Propagation movie (local, also online from Texas A&M University<= /st1:PlaceType>). Shows Plant Tissue Culture techniques being used in a commercial nursery in= Texas. Very good= .

      Tour of a micropropagation facility in Texas

      Date Pa= lm Tissue Culture Laboratory from Zvieli nursery Israel. Click on the Video To= ur – shows stages of tissue culture of date palms. Nice.

      Kitchen Curture= Kits, showing micropropagation of African Violet plants in a school laboratory. S= ome good photos.

      Plant Tissue Culture Information Exchange site.

Cloning Anima= ls

      Cl= oning Dolly from Starr. OK.

      Roslin Institure – Home of Dolly

      Click = and Clone from Utah. Clone your own mice. Great fun.

      Cloning from Beep. Et= hical issues of animal and human therapeutic cloning. Nice, but not really releva= nt.

Sexu= al Reproduction

Sperm

      Sperm and Egg anatomy from Vodopich (also from Mader). Drag and drop. Simple.

      Spermatogenesis from Starr also another one!

      Sperm production from ADAM

      S= permatogenesis from McGraw-Hill (local)

      Sperm an= d egg images from 3dscience

Eggs

      Oogenesis from Starr

      Egg cell production from ADAM

      Egg production from ADAM

      O= ogenesis from McGraw-Hill (local)

Fertilisation=

      Fertilisation in humans from Starr. More detailed than needed, but interesting.

      Fertilisation article from 3dscience

      Plant reproduction from Starr. Covers everything in more detail than needed, = but interesting. Also a shorter version.

      IVF from ABC Australia<= /st1:place>

Sexual Life c= ycles

      Life cycle of a conifer from Starr

      Life cycle of a fern from Starr.

      Life cycle of a moss from Starr

      L= ife cycle of an alga from Starr

      Life cycle of a fungus from Starr

      Life cycle of Chlamydomonas from Starr

      Alternation of generations from J Kimball

Embryo Development

Not needed, b= ut quite interesting

      Frog emb= ryo development from Alberts ECB (local)

      Embryonic ori= gin from Alberts ECB (local)

      Zebrafish embryo development from Alberts ECB (local)

      Drosophila development from Alberts ECB (local)

      Sea Urchin fertilisation from Alberts ECB (local)

      Embryo development (local from Benjamin Cummings)

      = Frog cycle from Starr

      Bird embryo development from Starr

      Neural tube development from Starr

      = Apoptosis movie in human hand development from Starr

Genetic Engineering Techniques=

General<= /o:p>

      GFR’s powerpoint summarising genetic engineering.

      = Genetic engineering techniques for mice 10-minute movie from HHMI.

      Introduction to Genetic Engineering from DNAi (choose Manipulation-Revolution-Problem)

      Genetic Engineerin= g from MIT Biology Hypertextbook. Good for detailed background information for teachers.

      Genetic Engine= ering questions and answers from David Silverman’s Big Biology Book. Go= od for student research.

      Cloning techniques from Boyer (choose cloning). Odd interactive animation of ma= ny techniques.

      Genetic Engineering from AS Guru

      Genetic enginee= ring from DNA from the beginning.

PCR

      PCR from Suamans. Very good introduction, similar to Raven.

      PCR from Raven. Very good, fairly simple summary. Similar to Sumanas. Also from= Mader.

      PCR from Starr

      PCR (2D) from DNAi (choose Manipulation-Techniques-Amplifying-2D) Interactive PCR, with g= raph showing output.

      PCR (3D) from DNAi (choose Manipulation-Techniques-Amplifying-3D). very nice animation – best.

      PCR from Alberts ECB2 (local)

      PC= R from Alberts MCB3 (local). Very detailed and good for background but too tedious for students.

      PCR from Boyer (choose PCR).

      PCR from Lehninger

      PCR (local). Bit simple, not worth using.

      Eye of = the Donkey – PCR game from Nobel Prize.org. A bit silly.

Electrophoresis

      Electrophore= sis of DNA from University of Massachusets MyD= NA. Nice simple interactive explanation. Good starter.

      Electrophoresis of DNA from DNAi (choose Manipulatio= n-Techniques-Sorting and Sequencing-Gel Electrophoresis) Step-by-step guide. Best.

      Electrophoresis of DNA local from Sumanas and on= -line from LifeWire (and from 8^th ed). Very good. Best.

      Electrophoresis (general) from Lehninger

      Electrophoresis of DNA digest from Boyer.

      Electrophor= esis of DNA digest from DJ Good. Just showing a run, but illustrates results= of DNA digestion nicely.

      DNA Electrophoresis and Southern Blot animation from Raven. Not really relevant.

      Electrophoresis of Protein from Stryer. Nice animation, but not DNA.

      Electrophoresis of protein from Lehninger V. good.

      DNA fingerprinting. Exe file doesn’t work

      DNA fingerprinting from Raven (choose RFLP)

      Paternity testing by DNA fingerprinting from Sumanas.

Sequencing DNA

      Sanger Sequencing from DNAi (choose Manipulation-Tec= hniques-Sorting and Sequencing-Early sequencing)

      Cycle Sequencing from DNAi (choose Manipulation-Tech= niques-Sorting and Sequencing-Cycle sequencing)

      DNA sequencing from Lehninger (local). Quite technical.

      DNA sequencing from Starr

      DNA sequencing from Lehninger

      DNA sequencing<= /a> from DNA from the beginning.

Cutting and Pasting DNA

      Restriction Enzyme from Raven. Good introduction to Restriction enzymes and ligase action. Also from Mader.

      Cutting and Pasting DNA from DNAi (choose Manipulati= on-Techniques-Cutting and Pasting-Recombining DNA). Nice 3D animation of restriction enzyme and ligase.

      Cutting and Pasting DNA into a plasmid from Raven. Also from Mader.

      Restriction E= nzyme catalogue from New England Biolabs. Illustrates variety of recognition sites. Also contain plasmid sequence maps (see DNA sequences and map on left menu).

      Gene splicing game from Mader. Choose the correct restriction enzyme (itR= 17;s E!).

      Molecular Biology Lab from The B= iology Place. How to do a bacterial transformation in= the lab. Quite nice.

      Plasmid cloning from Lehninger

      Cutting and pasting human DNA from Benjamin Cummings (local). Very similar to Raven, but not as pretty.

            Restriction Enzymes from Benjamin Cummings (local). Quite detailed, but not as good= as Raven.

      Recombinant DNA from Starr

      Restriction enzymes from Starr, showing recognition sites of 3 enzymes

      DNA Fingerprinting from Johnson Explorations

      Making a restriction map from Johnson Explorations

      Recombinant DNA an= imation from University of Delaware. Simple= .

Transforming Cells

      Transforming Bacterial Cells from DNAi (choose Manipulation-Techniques-Transferring and Storing-Transformation). Short animation about using heat shock to actually get a plasmid across a bacteri= al cell membrane.

      Microinjection movies. First into an egg nucleus; second = into a nematode worm. (l= ocal)

      Inserting DNA into plant cells from Raven (choose the Ti plasmid). Nice.

      Ti Plasmid from Starr

Selecting and Growing transformed Cells

      = Cloning DNA in bacteria from Alberts (local) and on-line from Sumanas. Very nice, using R plasmids and growing bacterial colonie= s.

      Inserting human DNA into bacteria from Raven (choose Early Genetic Engineering Experiment). Good for showing how different recombinant plasmids are formed= and how antibiotic resistance is used.

      Inserting Human DNA into bacteria cells (from Sumanas). Quite nice, but not as go= od as others.

      Inserting DNA into other organisms from DNAi (choose Manipulation-Techniques-Model Organisms). Simple, fun overview of different organisms used in genetic engineering.

Biotechnology Fermenters

      Genentech Tour from DNAi (choose Manipulation-Produc= tion-Putting it together). Good idea of industrial-scale fermenters.

Other Genetic Engineering Techniques

      Putting = DNA to Work. A variety of interactive activities from the Koshland Science Museum. Look nice, = but not sure of relevance.

      cDNA movie from Lehninger. Not very relevant.

      DNA chips local (from Sumanas) and on= -line from LifeWire (and 8^th ed). Not very relevant.

      DNA microarray chip animation from Raven (choose Microarray)

      Making vaccines animation from Raven (Module 7!)

      Introns, Exons and cDNA animation from Raven

      Rever= se Transcriptase and cDNA from Starr

      DNA probes from Starr

      DNA mi= croarray animation from Davidson

Genetic Engineering Applications

Insulin<= /o:p>

      Insulin from Bacteria from DNAi (choose Manipulation= -Production-Putting it together)

      Insulin from Yeast from DNAi (choose Manipulation-Pr= oduction-Putting it together)

      Humulin factshee= t from the company that makes genetically-engineered insulin.

      Insulin factsheets from Dibetes UK

Pharming=

      Rosli= n Institute. Where Dolly was made. Background information and photos.

      Essay on Pharming from Biotech monitor. Good for history of pharming.

      GM Proteins from BEEP=

GM crops=

      GM crops from Beep

      Genetically modified foods from CSA

General Biote= chnology

      A= GBIOS – News and information about biotechnology

      Biolink – News, information and resources about biotechnology

      Nature.ca – Various biotechnology stuff

      BioN= ews from Progress Educational Trust

      Biotechnology Monitor=

      Create a DNA fi= ngerprint from Nova

Gene= Therapy

Cystic Fibros= is

      Menacing Mucus (local). Also online from Starr – very big download. Cystic Fibrosis movie

      Cystic Fibrosis from Your Genes Your Health (Dolan Learning Centre)

      = Cystic Fibrosis from School Science

      Custic Fibrosis from Johnson Explorations

General Gene = Therapy

      Gene Therapy from Bee= p

      Genes and Disease from NCBI

      Your Genes,= Your Health from Dolan DNA lab

      = Learn.Genetics from University of Utah

      Cracking the Code from Nova

      What can= our chromosomes tell us? from Learn genetics at University of Utah<= /st1:PlaceName>

      Gene Therapy= from Learn genetics at Univers= ity of Utah

      Space Doctor from Learn genetics at University of Utah

      Your Genes, your choices from ORNL

      Huntin= ton’s disease from Stanford HOPES

Huma= n Genome Project

      Se= quencing the Genome from LifeWire.

      Human Genome Website from the US Dept of Energy.

      Human genome Brochure from NIH (local pdf file)

      HGP Ethics Movie= from NIH (local movie)

      HGP advertis= ement from NIH (local movie)

      Ethics and the Gene Map from Simply Science.

      Your = Genome.

      Official Human genome map from Entrez/NCBI

      International HapMap Project

      Human Genome Project Educational resources from NHGRI

      Human genome map from NCBI

      NCBI map viewer

      NCBI home page

      Your genome.org from the Sanger Institute

      Sanger = Centre

      Genes and Diseases from NCBI

      Genetics Education Centre from University of Kansas

      Human genome Landmarks from US DOE

      The HGP site

Written by Neil C Millar, Heckmondwike Grammar School. nmillar@heckgrammar.ki= rlklees.sch.uk. Last updated May 2007.